diff --git a/isthmus-cli/src/main/java/io/substrait/isthmus/cli/IsthmusEntryPoint.java b/isthmus-cli/src/main/java/io/substrait/isthmus/cli/IsthmusEntryPoint.java
index c8726c387..58a7e123f 100644
--- a/isthmus-cli/src/main/java/io/substrait/isthmus/cli/IsthmusEntryPoint.java
+++ b/isthmus-cli/src/main/java/io/substrait/isthmus/cli/IsthmusEntryPoint.java
@@ -10,6 +10,7 @@
 import io.substrait.isthmus.SqlExpressionToSubstrait;
 import io.substrait.isthmus.SqlToSubstrait;
 import io.substrait.isthmus.sql.SubstraitCreateStatementParser;
+import io.substrait.plan.PlanProtoConverter;
 import io.substrait.proto.ExtendedExpression;
 import io.substrait.proto.Plan;
 import java.io.IOException;
@@ -94,7 +95,7 @@ public Integer call() throws Exception {
       Prepare.CatalogReader catalog =
           SubstraitCreateStatementParser.processCreateStatementsToCatalog(
               createStatements.toArray(String[]::new));
-      Plan plan = converter.execute(sql, catalog);
+      Plan plan = new PlanProtoConverter().toProto(converter.convert(sql, catalog));
       printMessage(plan);
     }
     return 0;
diff --git a/isthmus/src/main/java/io/substrait/isthmus/SqlToSubstrait.java b/isthmus/src/main/java/io/substrait/isthmus/SqlToSubstrait.java
index 8a5e19bf8..e901397d1 100644
--- a/isthmus/src/main/java/io/substrait/isthmus/SqlToSubstrait.java
+++ b/isthmus/src/main/java/io/substrait/isthmus/SqlToSubstrait.java
@@ -3,9 +3,9 @@
 import com.google.common.annotations.VisibleForTesting;
 import io.substrait.isthmus.sql.SubstraitSqlValidator;
 import io.substrait.plan.ImmutablePlan.Builder;
+import io.substrait.plan.Plan;
 import io.substrait.plan.Plan.Version;
 import io.substrait.plan.PlanProtoConverter;
-import io.substrait.proto.Plan;
 import java.util.List;
 import org.apache.calcite.plan.hep.HepPlanner;
 import org.apache.calcite.plan.hep.HepProgram;
@@ -31,35 +31,51 @@ public SqlToSubstrait(FeatureBoard features) {
     super(features);
   }
 
-  public Plan execute(String sql, Prepare.CatalogReader catalogReader) throws SqlParseException {
-    SqlValidator validator = new SubstraitSqlValidator(catalogReader);
-    return executeInner(sql, validator, catalogReader);
-  }
-
-  List<RelRoot> sqlToRelNode(String sql, Prepare.CatalogReader catalogReader)
+  /**
+   * Converts a SQL statements string into a Substrait proto {@link io.substrait.proto.Plan}.
+   *
+   * @param sql the SQL statements string containing one more SQL statements
+   * @param catalogReader the {@link Prepare.CatalogReader} for finding tables/views referenced in
+   *     the SQL statements string
+   * @return the Substrait proto {@link io.substrait.proto.Plan}
+   * @throws SqlParseException if there is an error while parsing the SQL statements string
+   * @deprecated use {@link #convert(String, org.apache.calcite.prepare.Prepare.CatalogReader)}
+   *     instead to get a {@link Plan} and convert that to a {@link io.substrait.proto.Plan} using
+   *     {@link PlanProtoConverter#toProto(Plan)}
+   */
+  @Deprecated
+  public io.substrait.proto.Plan execute(String sql, Prepare.CatalogReader catalogReader)
       throws SqlParseException {
-    SqlValidator validator = new SubstraitSqlValidator(catalogReader);
-    return sqlToRelNode(sql, validator, catalogReader);
+    PlanProtoConverter planToProto = new PlanProtoConverter();
+
+    return planToProto.toProto(convert(sql, catalogReader));
   }
 
-  private Plan executeInner(String sql, SqlValidator validator, Prepare.CatalogReader catalogReader)
-      throws SqlParseException {
+  /**
+   * Converts a SQL statements string into a Substrait {@link Plan}.
+   *
+   * @param sql the SQL statements string containing one more SQL statements
+   * @param catalogReader the {@link Prepare.CatalogReader} for finding tables/views referenced in
+   *     the SQL statements string
+   * @return the Substrait {@link Plan}
+   * @throws SqlParseException if there is an error while parsing the SQL statements string
+   */
+  public Plan convert(String sql, Prepare.CatalogReader catalogReader) throws SqlParseException {
     Builder builder = io.substrait.plan.Plan.builder();
     builder.version(Version.builder().from(Version.DEFAULT_VERSION).producer("isthmus").build());
 
     // TODO: consider case in which one sql passes conversion while others don't
-    sqlToRelNode(sql, validator, catalogReader).stream()
+    sqlToRelNode(sql, catalogReader).stream()
         .map(root -> SubstraitRelVisitor.convert(root, EXTENSION_COLLECTION, featureBoard))
         .forEach(root -> builder.addRoots(root));
 
-    PlanProtoConverter planToProto = new PlanProtoConverter();
-
-    return planToProto.toProto(builder.build());
+    return builder.build();
   }
 
-  private List<RelRoot> sqlToRelNode(
-      String sql, SqlValidator validator, Prepare.CatalogReader catalogReader)
+  @VisibleForTesting
+  List<RelRoot> sqlToRelNode(String sql, Prepare.CatalogReader catalogReader)
       throws SqlParseException {
+    SqlValidator validator = new SubstraitSqlValidator(catalogReader);
     SqlParser parser = SqlParser.create(sql, parserConfig);
     SqlNodeList parsedList = parser.parseStmtList();
     SqlToRelConverter converter = createSqlToRelConverter(validator, catalogReader);
@@ -70,8 +86,7 @@ private List<RelRoot> sqlToRelNode(
     return roots;
   }
 
-  @VisibleForTesting
-  SqlToRelConverter createSqlToRelConverter(
+  protected SqlToRelConverter createSqlToRelConverter(
       SqlValidator validator, Prepare.CatalogReader catalogReader) {
     SqlToRelConverter converter =
         new SqlToRelConverter(
@@ -84,8 +99,7 @@ SqlToRelConverter createSqlToRelConverter(
     return converter;
   }
 
-  @VisibleForTesting
-  static RelRoot getBestExpRelRoot(SqlToRelConverter converter, SqlNode parsed) {
+  protected RelRoot getBestExpRelRoot(SqlToRelConverter converter, SqlNode parsed) {
     RelRoot root = converter.convertQuery(parsed, true, true);
     {
       // RelBuilder seems to implicitly use the rule below,
diff --git a/isthmus/src/test/java/io/substrait/isthmus/ApplyJoinPlanTest.java b/isthmus/src/test/java/io/substrait/isthmus/ApplyJoinPlanTest.java
index 8fb704977..7804c2b46 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/ApplyJoinPlanTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/ApplyJoinPlanTest.java
@@ -62,7 +62,7 @@ public void lateralJoinQuery() throws SqlParseException {
     SqlToSubstrait sE2E = new SqlToSubstrait();
     Assertions.assertThrows(
         UnsupportedOperationException.class,
-        () -> sE2E.execute(sql, TPCDS_CATALOG),
+        () -> sE2E.convert(sql, TPCDS_CATALOG),
         "Lateral join is not supported");
   }
 
@@ -83,7 +83,7 @@ public void outerApplyQuery() throws SqlParseException {
     // TODO validate end to end conversion
     Assertions.assertThrows(
         UnsupportedOperationException.class,
-        () -> new SqlToSubstrait().execute(sql, TPCDS_CATALOG),
+        () -> new SqlToSubstrait().convert(sql, TPCDS_CATALOG),
         "APPLY is not supported");
   }
 
@@ -123,7 +123,7 @@ public void nestedApplyJoinQuery() throws SqlParseException {
     // TODO validate end to end conversion
     Assertions.assertThrows(
         UnsupportedOperationException.class,
-        () -> new SqlToSubstrait().execute(sql, TPCDS_CATALOG),
+        () -> new SqlToSubstrait().convert(sql, TPCDS_CATALOG),
         "APPLY is not supported");
   }
 
@@ -138,7 +138,7 @@ public void crossApplyQuery() throws SqlParseException {
     // TODO validate end to end conversion
     Assertions.assertThrows(
         UnsupportedOperationException.class,
-        () -> new SqlToSubstrait().execute(sql, TPCDS_CATALOG),
+        () -> new SqlToSubstrait().convert(sql, TPCDS_CATALOG),
         "APPLY is not supported");
   }
 }
diff --git a/isthmus/src/test/java/io/substrait/isthmus/KeyConstraintsTest.java b/isthmus/src/test/java/io/substrait/isthmus/KeyConstraintsTest.java
index 7c43502d9..ff00123bb 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/KeyConstraintsTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/KeyConstraintsTest.java
@@ -14,6 +14,6 @@ public void tpcds(int query) throws Exception {
     String values = asString("keyconstraints_schema.sql");
     Prepare.CatalogReader catalog =
         SubstraitCreateStatementParser.processCreateStatementsToCatalog(values);
-    s.execute(asString(String.format("tpcds/queries/%02d.sql", query)), catalog);
+    s.convert(asString(String.format("tpcds/queries/%02d.sql", query)), catalog);
   }
 }
diff --git a/isthmus/src/test/java/io/substrait/isthmus/NameRoundtripTest.java b/isthmus/src/test/java/io/substrait/isthmus/NameRoundtripTest.java
index ee89f608c..6eb89cbdf 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/NameRoundtripTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/NameRoundtripTest.java
@@ -25,14 +25,10 @@ void preserveNamesFromSql() throws Exception {
     String query = "SELECT \"a\", \"B\" FROM foo GROUP BY a, b";
     List<String> expectedNames = List.of("a", "B");
 
-    List<org.apache.calcite.rel.RelRoot> calciteRelRoots = s.sqlToRelNode(query, catalogReader);
-    assertEquals(1, calciteRelRoots.size());
+    Plan plan = s.convert(query, catalogReader);
+    assertEquals(1, plan.getRoots().size());
 
-    org.apache.calcite.rel.RelRoot calciteRelRoot1 = calciteRelRoots.get(0);
-    assertEquals(expectedNames, calciteRelRoot1.validatedRowType.getFieldNames());
-
-    io.substrait.plan.Plan.Root substraitRelRoot =
-        SubstraitRelVisitor.convert(calciteRelRoot1, EXTENSION_COLLECTION);
+    io.substrait.plan.Plan.Root substraitRelRoot = plan.getRoots().get(0);
     assertEquals(expectedNames, substraitRelRoot.getNames());
 
     org.apache.calcite.rel.RelRoot calciteRelRoot2 = substraitToCalcite.convert(substraitRelRoot);
diff --git a/isthmus/src/test/java/io/substrait/isthmus/NestedStructQueryTest.java b/isthmus/src/test/java/io/substrait/isthmus/NestedStructQueryTest.java
index e645f29cb..05aa5944f 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/NestedStructQueryTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/NestedStructQueryTest.java
@@ -60,7 +60,7 @@ private void test(Table table, String query, String expectedExpressionText)
     final Schema schema = new SubstraitSchema(Map.of("my_table", table));
     final CalciteCatalogReader catalog = schemaToCatalog("nested", schema);
     final SqlToSubstrait sqlToSubstrait = new SqlToSubstrait();
-    Plan plan = sqlToSubstrait.execute(query, catalog);
+    Plan plan = toProto(sqlToSubstrait.convert(query, catalog));
     Expression obtainedExpression =
         plan.getRelations(0).getRoot().getInput().getProject().getExpressions(0);
     Expression expectedExpression = TextFormat.parse(expectedExpressionText, Expression.class);
diff --git a/isthmus/src/test/java/io/substrait/isthmus/PlanTestBase.java b/isthmus/src/test/java/io/substrait/isthmus/PlanTestBase.java
index 27ae7eea9..8bac5d854 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/PlanTestBase.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/PlanTestBase.java
@@ -87,24 +87,26 @@ protected Plan assertProtoPlanRoundrip(String query, SqlToSubstrait s, String cr
   protected Plan assertProtoPlanRoundrip(
       String query, SqlToSubstrait s, Prepare.CatalogReader catalogReader)
       throws SqlParseException {
-    io.substrait.proto.Plan protoPlan1 = s.execute(query, catalogReader);
-    Plan plan = new ProtoPlanConverter(extensions).from(protoPlan1);
-    io.substrait.proto.Plan protoPlan2 = new PlanProtoConverter().toProto(plan);
+    Plan plan1 = s.convert(query, catalogReader);
+    io.substrait.proto.Plan protoPlan1 = toProto(plan1);
+
+    Plan plan2 = new ProtoPlanConverter(extensions).from(protoPlan1);
+    io.substrait.proto.Plan protoPlan2 = toProto(plan2);
     assertEquals(protoPlan1, protoPlan2);
-    List<RelRoot> rootRels = s.sqlToRelNode(query, catalogReader);
-    assertEquals(rootRels.size(), plan.getRoots().size());
-    for (int i = 0; i < rootRels.size(); i++) {
-      Plan.Root rootRel = SubstraitRelVisitor.convert(rootRels.get(i), extensions);
+
+    assertEquals(plan1.getRoots().size(), plan2.getRoots().size());
+    for (int i = 0; i < plan1.getRoots().size(); i++) {
       assertEquals(
-          rootRel.getInput().getRecordType(), plan.getRoots().get(i).getInput().getRecordType());
+          plan1.getRoots().get(i).getInput().getRecordType(),
+          plan2.getRoots().get(i).getInput().getRecordType());
     }
-    return plan;
+
+    return plan2;
   }
 
   protected void assertPlanRoundtrip(Plan plan) {
-    io.substrait.proto.Plan protoPlan1 = new PlanProtoConverter().toProto(plan);
-    io.substrait.proto.Plan protoPlan2 =
-        new PlanProtoConverter().toProto(new ProtoPlanConverter().from(protoPlan1));
+    io.substrait.proto.Plan protoPlan1 = toProto(plan);
+    io.substrait.proto.Plan protoPlan2 = toProto(new ProtoPlanConverter().from(protoPlan1));
     assertEquals(protoPlan1, protoPlan2);
   }
 
@@ -129,13 +131,11 @@ protected RelRoot assertSqlSubstraitRelRoundTrip(
 
     SqlToSubstrait s = new SqlToSubstrait();
 
-    // 1. SQL -> Calcite RelRoot
-    List<RelRoot> relRoots = s.sqlToRelNode(query, catalogReader);
-    assertEquals(1, relRoots.size());
-    RelRoot relRoot1 = relRoots.get(0);
+    // 1. SQL -> Substrait Plan
+    Plan plan1 = s.convert(query, catalogReader);
 
-    // 2. Calcite RelRoot  -> Substrait Rel
-    Plan.Root pojo1 = SubstraitRelVisitor.convert(relRoot1, extensions);
+    // 2. Substrait Plan  -> Substrait Rel
+    Plan.Root pojo1 = plan1.getRoots().get(0);
 
     // 3. Substrait Rel -> Calcite RelNode
     RelRoot relRoot2 = substraitToCalcite.convert(pojo1);
@@ -178,37 +178,36 @@ protected void assertFullRoundTrip(String sqlQuery, Prepare.CatalogReader catalo
     SqlToSubstrait sqlConverter = new SqlToSubstrait();
     ExtensionCollector extensionCollector = new ExtensionCollector();
 
-    // SQL -> Calcite 1
-    List<RelRoot> relRoots = sqlConverter.sqlToRelNode(sqlQuery, catalogReader);
-    assertEquals(1, relRoots.size());
-    RelRoot calcite1 = relRoots.get(0);
+    // SQL -> Substrait Plan 1
+    Plan plan1 = sqlConverter.convert(sqlQuery, catalogReader);
+    assertEquals(1, plan1.getRoots().size());
 
-    // Calcite 1 -> Substrait POJO 1
-    Plan.Root pojo1 = SubstraitRelVisitor.convert(calcite1, extensions);
+    // Substrait Plan 1 -> Substrait Root 1
+    Plan.Root root1 = plan1.getRoots().get(0);
 
-    // Substrait POJO 1 -> Substrait Proto
-    io.substrait.proto.RelRoot proto = new RelProtoConverter(extensionCollector).toProto(pojo1);
+    // Substrait Root 1 -> Substrait Proto
+    io.substrait.proto.RelRoot proto = new RelProtoConverter(extensionCollector).toProto(root1);
 
-    // Substrait Proto -> Substrait Pojo 2
-    Plan.Root pojo2 = new ProtoRelConverter(extensionCollector, extensions).from(proto);
+    // Substrait Proto -> Substrait Root 2
+    Plan.Root root2 = new ProtoRelConverter(extensionCollector, extensions).from(proto);
 
-    // Verify that POJOs are the same
-    assertEquals(pojo1, pojo2);
+    // Verify that roots are the same
+    assertEquals(root1, root2);
 
-    // Substrait POJO 2 -> Calcite 2
+    // Substrait Root 2 -> Calcite 2
     final SubstraitToCalcite substraitToCalcite =
         new SubstraitToCalcite(extensions, typeFactory, catalogReader);
 
-    RelRoot calcite2 = substraitToCalcite.convert(pojo2);
+    RelRoot calcite2 = substraitToCalcite.convert(root2);
     // It would be ideal to compare calcite1 and calcite2, however there isn't a good mechanism to
     // do so
     assertNotNull(calcite2);
 
-    // Calcite 2 -> Substrait POJO 3
-    Plan.Root pojo3 = SubstraitRelVisitor.convert(calcite2, extensions);
+    // Calcite 2 -> Substrait Root 3
+    Plan.Root root3 = SubstraitRelVisitor.convert(calcite2, extensions);
 
     // Verify that POJOs are the same
-    assertEquals(pojo1, pojo3);
+    assertEquals(root1, root3);
   }
 
   /**
@@ -285,9 +284,9 @@ protected void assertRowMatch(RelDataType actual, List<Type> expected) {
     assertEquals(expected, struct.fields());
   }
 
-  protected io.substrait.proto.Plan toSubstraitPlan(String sql, CalciteCatalogReader catalog)
+  protected Plan toSubstraitPlan(String sql, CalciteCatalogReader catalog)
       throws SqlParseException {
-    return new SqlToSubstrait().execute(sql, catalog);
+    return new SqlToSubstrait().convert(sql, catalog);
   }
 
   protected String toSql(io.substrait.proto.Plan protoPlan) {
@@ -305,6 +304,10 @@ protected String toSql(Plan plan) {
     return SubstraitSqlDialect.toSql(project).getSql();
   }
 
+  protected io.substrait.proto.Plan toProto(Plan plan) {
+    return new PlanProtoConverter().toProto(plan);
+  }
+
   protected static CalciteCatalogReader schemaToCatalog(String schemaName, Schema schema) {
     CalciteSchema rootSchema = CalciteSchema.createRootSchema(false);
     rootSchema.add(schemaName, schema);
diff --git a/isthmus/src/test/java/io/substrait/isthmus/ProtoPlanConverterTest.java b/isthmus/src/test/java/io/substrait/isthmus/ProtoPlanConverterTest.java
index 6d033b809..54af92458 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/ProtoPlanConverterTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/ProtoPlanConverterTest.java
@@ -4,7 +4,6 @@
 
 import io.substrait.isthmus.utils.SetUtils;
 import io.substrait.plan.Plan;
-import io.substrait.plan.PlanProtoConverter;
 import io.substrait.plan.ProtoPlanConverter;
 import io.substrait.proto.AggregateFunction;
 import io.substrait.relation.Cross;
@@ -23,7 +22,7 @@ public class ProtoPlanConverterTest extends PlanTestBase {
 
   private io.substrait.proto.Plan getProtoPlan(String query1) throws SqlParseException {
     SqlToSubstrait s = new SqlToSubstrait();
-    return s.execute(query1, TPCH_CATALOG);
+    return toProto(s.convert(query1, TPCH_CATALOG));
   }
 
   @Test
@@ -54,8 +53,7 @@ public void distinctCount() throws IOException, SqlParseException {
     String distinctQuery = "select count(DISTINCT L_ORDERKEY) from lineitem";
     io.substrait.proto.Plan protoPlan = getProtoPlan(distinctQuery);
     assertAggregateInvocationDistinct(protoPlan);
-    assertAggregateInvocationDistinct(
-        new PlanProtoConverter().toProto(new ProtoPlanConverter().from(protoPlan)));
+    assertAggregateInvocationDistinct(toProto(new ProtoPlanConverter().from(protoPlan)));
   }
 
   @Test
diff --git a/isthmus/src/test/java/io/substrait/isthmus/RelCopyOnWriteVisitorTest.java b/isthmus/src/test/java/io/substrait/isthmus/RelCopyOnWriteVisitorTest.java
index 6e95e3dcd..973f8829d 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/RelCopyOnWriteVisitorTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/RelCopyOnWriteVisitorTest.java
@@ -9,7 +9,6 @@
 import io.substrait.extension.SimpleExtension;
 import io.substrait.isthmus.sql.SubstraitSqlDialect;
 import io.substrait.plan.Plan;
-import io.substrait.plan.ProtoPlanConverter;
 import io.substrait.relation.Aggregate;
 import io.substrait.relation.CopyOnWriteUtils;
 import io.substrait.relation.NamedScan;
@@ -77,8 +76,7 @@ public class RelCopyOnWriteVisitorTest extends PlanTestBase {
 
   private Plan buildPlanFromQuery(String query) throws IOException, SqlParseException {
     SqlToSubstrait s = new SqlToSubstrait();
-    io.substrait.proto.Plan protoPlan1 = s.execute(query, TPCH_CATALOG);
-    return new ProtoPlanConverter().from(protoPlan1);
+    return s.convert(query, TPCH_CATALOG);
   }
 
   @Test
diff --git a/isthmus/src/test/java/io/substrait/isthmus/SubqueryPlanTest.java b/isthmus/src/test/java/io/substrait/isthmus/SubqueryPlanTest.java
index 23a946d92..9fcba2cc0 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/SubqueryPlanTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/SubqueryPlanTest.java
@@ -18,9 +18,10 @@ public class SubqueryPlanTest extends PlanTestBase {
   public void existsCorrelatedSubquery() throws SqlParseException {
     SqlToSubstrait s = new SqlToSubstrait();
     Plan plan =
-        s.execute(
-            "select l_partkey from lineitem where exists (select o_orderdate from orders where o_orderkey = l_orderkey)",
-            TPCH_CATALOG);
+        toProto(
+            s.convert(
+                "select l_partkey from lineitem where exists (select o_orderdate from orders where o_orderkey = l_orderkey)",
+                TPCH_CATALOG));
 
     Expression.Subquery subquery =
         plan.getRelations(0)
@@ -59,9 +60,10 @@ public void existsCorrelatedSubquery() throws SqlParseException {
   public void uniqueCorrelatedSubquery() throws IOException, SqlParseException {
     SqlToSubstrait s = new SqlToSubstrait();
     Plan plan =
-        s.execute(
-            "select l_partkey from lineitem where unique (select o_orderdate from orders where o_orderkey = l_orderkey)",
-            TPCH_CATALOG);
+        toProto(
+            s.convert(
+                "select l_partkey from lineitem where unique (select o_orderdate from orders where o_orderkey = l_orderkey)",
+                TPCH_CATALOG));
 
     Expression.Subquery subquery =
         plan.getRelations(0)
@@ -104,7 +106,7 @@ public void inPredicateCorrelatedSubQuery() throws IOException, SqlParseExceptio
     SqlToSubstrait s = new SqlToSubstrait();
     String sql =
         "select l_orderkey from lineitem where l_partkey in (select p_partkey from part where p_partkey = l_partkey)";
-    Plan plan = s.execute(sql, TPCH_CATALOG);
+    Plan plan = toProto(s.convert(sql, TPCH_CATALOG));
 
     Expression.Subquery subquery =
         plan.getRelations(0)
@@ -142,7 +144,7 @@ public void notInPredicateCorrelatedSubquery() throws IOException, SqlParseExcep
     SqlToSubstrait s = new SqlToSubstrait();
     String sql =
         "select l_orderkey from lineitem where l_partkey not in (select p_partkey from part where p_partkey = l_partkey)";
-    Plan plan = s.execute(sql, TPCH_CATALOG);
+    Plan plan = toProto(s.convert(sql, TPCH_CATALOG));
     Expression.Subquery subquery =
         plan.getRelations(0)
             .getRoot()
@@ -192,7 +194,7 @@ public void existsNestedCorrelatedSubquery() throws IOException, SqlParseExcepti
             + "          FROM partsupp ps\n"
             + "          WHERE ps.ps_partkey = p.p_partkey\n"
             + "          AND   PS.ps_suppkey = l.l_suppkey))";
-    Plan plan = s.execute(sql, TPCH_CATALOG);
+    Plan plan = toProto(s.convert(sql, TPCH_CATALOG));
 
     Expression.Subquery outer_subquery =
         plan.getRelations(0)
@@ -266,7 +268,7 @@ public void existsNestedCorrelatedSubquery() throws IOException, SqlParseExcepti
   public void nestedScalarCorrelatedSubquery() throws IOException, SqlParseException {
     SqlToSubstrait s = new SqlToSubstrait();
     String sql = asString("subquery/nested_scalar_subquery_in_filter.sql");
-    Plan plan = s.execute(sql, TPCH_CATALOG);
+    Plan plan = toProto(s.convert(sql, TPCH_CATALOG));
     String planText = JsonFormat.printer().includingDefaultValueFields().print(plan);
 
     System.out.println(planText);
@@ -344,7 +346,7 @@ public void correlatedScalarSubQInSelect() throws IOException {
     Assertions.assertThrows(
         UnsupportedOperationException.class,
         () -> {
-          s.execute(sql, TPCH_CATALOG);
+          s.convert(sql, TPCH_CATALOG);
         });
   }
 }
diff --git a/isthmus/src/test/java/io/substrait/isthmus/TpcdsQueryTest.java b/isthmus/src/test/java/io/substrait/isthmus/TpcdsQueryTest.java
index 9be238bc3..828ffab71 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/TpcdsQueryTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/TpcdsQueryTest.java
@@ -3,7 +3,7 @@
 import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
-import io.substrait.proto.Plan;
+import io.substrait.plan.Plan;
 import java.io.IOException;
 import java.util.Set;
 import java.util.stream.IntStream;
@@ -14,7 +14,8 @@
 /** TPC-DS test to convert SQL to Substrait and then convert those plans back to SQL. */
 public class TpcdsQueryTest extends PlanTestBase {
   private static final Set<Integer> toSubstraitExclusions = Set.of(9, 27, 36, 70, 86);
-  private static final Set<Integer> fromSubstraitExclusions = Set.of(1, 30, 67, 81);
+  private static final Set<Integer> fromSubstraitPojoExclusions = Set.of(1, 30, 81);
+  private static final Set<Integer> fromSubstraitProtoExclusions = Set.of(1, 30, 67, 81);
 
   static IntStream testCases() {
     return IntStream.rangeClosed(1, 99).filter(n -> !toSubstraitExclusions.contains(n));
@@ -29,12 +30,21 @@ static IntStream testCases() {
   public void testQuery(int query) throws IOException {
     String inputSql = asString(String.format("tpcds/queries/%02d.sql", query));
 
-    Plan plan = assertDoesNotThrow(() -> toSubstraitPlan(inputSql), "SQL to Substrait");
+    Plan plan = assertDoesNotThrow(() -> toSubstraitPlan(inputSql), "SQL to Substrait POJO");
 
-    if (!fromSubstraitExclusions.contains(query)) {
-      assertDoesNotThrow(() -> toSql(plan), "Substrait to SQL");
+    if (!fromSubstraitPojoExclusions.contains(query)) {
+      assertDoesNotThrow(() -> toSql(plan), "Substrait POJO to SQL");
     } else {
-      assertThrows(Throwable.class, () -> toSql(plan), "Substrait to SQL");
+      assertThrows(Throwable.class, () -> toSql(plan), "Substrait POJO to SQL");
+    }
+
+    io.substrait.proto.Plan proto =
+        assertDoesNotThrow(() -> toProto(plan), "Substrait POJO to Substrait PROTO");
+
+    if (!fromSubstraitProtoExclusions.contains(query)) {
+      assertDoesNotThrow(() -> toSql(proto), "Substrait PROTO to SQL");
+    } else {
+      assertThrows(Throwable.class, () -> toSql(proto), "Substrait PROTO to SQL");
     }
   }
 
diff --git a/isthmus/src/test/java/io/substrait/isthmus/TpchQueryTest.java b/isthmus/src/test/java/io/substrait/isthmus/TpchQueryTest.java
index 0a8b0e8af..1938689a1 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/TpchQueryTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/TpchQueryTest.java
@@ -2,7 +2,7 @@
 
 import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 
-import io.substrait.proto.Plan;
+import io.substrait.plan.Plan;
 import java.io.IOException;
 import java.util.stream.IntStream;
 import org.apache.calcite.sql.parser.SqlParseException;
@@ -24,9 +24,14 @@ static IntStream testCases() {
   public void testQuery(int query) throws IOException {
     String inputSql = asString(String.format("tpch/queries/%02d.sql", query));
 
-    Plan plan = assertDoesNotThrow(() -> toSubstraitPlan(inputSql), "SQL to Substrait");
+    Plan plan = assertDoesNotThrow(() -> toSubstraitPlan(inputSql), "SQL to Substrait POJO");
 
-    assertDoesNotThrow(() -> toSql(plan), "Substrait to SQL");
+    assertDoesNotThrow(() -> toSql(plan), "Substrait POJO to SQL");
+
+    io.substrait.proto.Plan proto =
+        assertDoesNotThrow(() -> toProto(plan), "Substrait POJO to Substrait PROTO");
+
+    assertDoesNotThrow(() -> toSql(proto), "Substrait PROTO to SQL");
   }
 
   private Plan toSubstraitPlan(String sql) throws SqlParseException {