diff --git a/agent/internal/agent/poller.go b/agent/internal/agent/poller.go
index 3423e48..c4d5410 100644
--- a/agent/internal/agent/poller.go
+++ b/agent/internal/agent/poller.go
@@ -6,11 +6,16 @@ import (
 	"log/slog"
 	"os"
 	"path/filepath"
+	"strings"
 
 	"github.com/TerrifiedBug/vectorflow/agent/internal/client"
 	"github.com/TerrifiedBug/vectorflow/agent/internal/config"
 )
 
+type configFetcher interface {
+	GetConfig() (*client.ConfigResponse, error)
+}
+
 type pipelineState struct {
 	checksum string
 	version  int
@@ -18,13 +23,13 @@ type pipelineState struct {
 
 type poller struct {
 	cfg            *config.Config
-	client         *client.Client
+	client         configFetcher
 	known          map[string]pipelineState // pipelineId -> last known state
 	sampleRequests []client.SampleRequestMsg
 	pendingAction  *client.PendingAction
 }
 
-func newPoller(cfg *config.Config, c *client.Client) *poller {
+func newPoller(cfg *config.Config, c configFetcher) *poller {
 	return &poller{
 		cfg:    cfg,
 		client: c,
@@ -146,6 +151,33 @@ func (p *poller) Poll() ([]PipelineAction, error) {
 		}
 	}
 
+	// Reconcile: remove any pipeline files on disk not in the server response.
+	// This catches orphans from previous enrollments or missed undeploys.
+	entries, readErr := os.ReadDir(pipelinesDir)
+	if readErr != nil {
+		slog.Warn("failed to read pipelines dir for reconciliation", "error", readErr)
+	} else {
+		for _, entry := range entries {
+			name := entry.Name()
+			if strings.HasSuffix(name, ".vf-metrics.yaml") {
+				continue
+			}
+			if !strings.HasSuffix(name, ".yaml") {
+				continue
+			}
+			id := strings.TrimSuffix(name, ".yaml")
+			if !seen[id] {
+				slog.Warn("removing orphaned pipeline config", "pipelineId", id)
+				if err := os.Remove(filepath.Join(pipelinesDir, name)); err != nil && !os.IsNotExist(err) {
+					slog.Warn("failed to remove orphaned pipeline config", "path", name, "error", err)
+				}
+				if err := os.Remove(filepath.Join(pipelinesDir, name+".vf-metrics.yaml")); err != nil && !os.IsNotExist(err) {
+					slog.Warn("failed to remove orphaned metrics sidecar", "path", name+".vf-metrics.yaml", "error", err)
+				}
+			}
+		}
+	}
+
 	// Store sample requests for the agent to process
 	p.sampleRequests = resp.SampleRequests
 
diff --git a/agent/internal/agent/poller_test.go b/agent/internal/agent/poller_test.go
new file mode 100644
index 0000000..2102e73
--- /dev/null
+++ b/agent/internal/agent/poller_test.go
@@ -0,0 +1,120 @@
+package agent
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/TerrifiedBug/vectorflow/agent/internal/client"
+	"github.com/TerrifiedBug/vectorflow/agent/internal/config"
+)
+
+type mockConfigFetcher struct {
+	resp *client.ConfigResponse
+}
+
+func (m *mockConfigFetcher) GetConfig() (*client.ConfigResponse, error) {
+	return m.resp, nil
+}
+
+func TestPoll_RemovesOrphanedPipelineFiles(t *testing.T) {
+	tmpDir := t.TempDir()
+	pipelinesDir := filepath.Join(tmpDir, "pipelines")
+	os.MkdirAll(pipelinesDir, 0700)
+
+	// Pre-existing files: one valid pipeline, one orphan, one orphan with metrics sidecar
+	os.WriteFile(filepath.Join(pipelinesDir, "pipeline-a.yaml"), []byte("valid"), 0600)
+	os.WriteFile(filepath.Join(pipelinesDir, "orphan-b.yaml"), []byte("stale"), 0600)
+	os.WriteFile(filepath.Join(pipelinesDir, "orphan-b.yaml.vf-metrics.yaml"), []byte("stale-metrics"), 0600)
+	os.WriteFile(filepath.Join(pipelinesDir, "orphan-c.yaml"), []byte("stale2"), 0600)
+	// Non-yaml file should be left alone
+	os.WriteFile(filepath.Join(pipelinesDir, "notes.txt"), []byte("keep"), 0600)
+
+	mc := &mockConfigFetcher{
+		resp: &client.ConfigResponse{
+			Pipelines: []client.PipelineConfig{
+				{
+					PipelineID:   "pipeline-a",
+					PipelineName: "Pipeline A",
+					ConfigYaml:   "valid",
+					Checksum:     "abc123",
+					Version:      1,
+				},
+			},
+		},
+	}
+
+	p := &poller{
+		cfg:    &config.Config{DataDir: tmpDir},
+		client: mc,
+		known:  make(map[string]pipelineState),
+	}
+
+	actions, err := p.Poll()
+	if err != nil {
+		t.Fatalf("Poll() error: %v", err)
+	}
+
+	// pipeline-a should be started (new to known map)
+	if len(actions) != 1 || actions[0].PipelineID != "pipeline-a" {
+		t.Errorf("expected 1 start action for pipeline-a, got %d actions", len(actions))
+	}
+
+	// pipeline-a.yaml should still exist
+	if _, err := os.Stat(filepath.Join(pipelinesDir, "pipeline-a.yaml")); err != nil {
+		t.Error("pipeline-a.yaml should exist")
+	}
+
+	// orphan-b.yaml and its metrics sidecar should be deleted
+	if _, err := os.Stat(filepath.Join(pipelinesDir, "orphan-b.yaml")); !os.IsNotExist(err) {
+		t.Error("orphan-b.yaml should be deleted")
+	}
+	if _, err := os.Stat(filepath.Join(pipelinesDir, "orphan-b.yaml.vf-metrics.yaml")); !os.IsNotExist(err) {
+		t.Error("orphan-b.yaml.vf-metrics.yaml should be deleted")
+	}
+
+	// orphan-c.yaml should be deleted
+	if _, err := os.Stat(filepath.Join(pipelinesDir, "orphan-c.yaml")); !os.IsNotExist(err) {
+		t.Error("orphan-c.yaml should be deleted")
+	}
+
+	// notes.txt (non-yaml) should be left alone
+	if _, err := os.Stat(filepath.Join(pipelinesDir, "notes.txt")); err != nil {
+		t.Error("notes.txt should still exist")
+	}
+}
+
+func TestPoll_EmptyResponseCleansAllFiles(t *testing.T) {
+	tmpDir := t.TempDir()
+	pipelinesDir := filepath.Join(tmpDir, "pipelines")
+	os.MkdirAll(pipelinesDir, 0700)
+
+	os.WriteFile(filepath.Join(pipelinesDir, "old-a.yaml"), []byte("stale"), 0600)
+	os.WriteFile(filepath.Join(pipelinesDir, "old-a.yaml.vf-metrics.yaml"), []byte("stale-metrics"), 0600)
+	os.WriteFile(filepath.Join(pipelinesDir, "old-b.yaml"), []byte("stale"), 0600)
+
+	mc := &mockConfigFetcher{
+		resp: &client.ConfigResponse{
+			Pipelines: []client.PipelineConfig{},
+		},
+	}
+
+	p := &poller{
+		cfg:    &config.Config{DataDir: tmpDir},
+		client: mc,
+		known:  make(map[string]pipelineState),
+	}
+
+	_, err := p.Poll()
+	if err != nil {
+		t.Fatalf("Poll() error: %v", err)
+	}
+
+	entries, _ := os.ReadDir(pipelinesDir)
+	for _, e := range entries {
+		if strings.HasSuffix(e.Name(), ".yaml") {
+			t.Errorf("expected all yaml files deleted, found: %s", e.Name())
+		}
+	}
+}