diff --git a/pkg/config/config.go b/pkg/config/config.go
index 6c339ec..69c0c71 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -58,6 +58,10 @@ func (c *Config) ValidateConfig() error {
 func Load(dir string, out io.Writer) (*Config, error) {
 	cfg := InitEmptyConfig()
 
+	if err := env.Parse(cfg); err != nil {
+		return nil, err
+	}
+
 	err := parseConfigFiles(dir, out, func(dir string) error {
 		return parseConfigFile(dir, cfg)
 	})
@@ -65,8 +69,6 @@ func Load(dir string, out io.Writer) (*Config, error) {
 		return nil, err
 	}
 
-	err = env.Parse(cfg)
-
 	return cfg, err
 }
 
@@ -282,13 +284,13 @@ func parseConfigFiles(dir string, out io.Writer, fn func(string) error) error {
 
 		parent = filepath.Dir(parent)
 	}
-	for i, file := range files {
+	for i, f := range files {
 		if i == 0 {
-			_, _ = fmt.Fprintln(out, tml.Sprintf("Parsing config from file: <green>'%s'</green>", file))
+			_, _ = fmt.Fprintln(out, tml.Sprintf("Parsing config from file: <green>'%s'</green>", f))
 		} else {
-			_, _ = fmt.Fprintln(out, tml.Sprintf("Merging with config from file: <green>'%s'</green>", file))
+			_, _ = fmt.Fprintln(out, tml.Sprintf("Merging with config from file: <green>'%s'</green>", f))
 		}
-		if err := fn(file); err != nil {
+		if err := fn(f); err != nil {
 			return err
 		}
 	}
diff --git a/pkg/config/config_test.go b/pkg/config/config_test.go
index a359667..69b7d37 100644
--- a/pkg/config/config_test.go
+++ b/pkg/config/config_test.go
@@ -36,6 +36,81 @@ func teardown(tempDir string) {
 	_ = os.RemoveAll(tempDir)
 }
 
+func TestLoad_Env_Overrides_YAML(t *testing.T) {
+	os.Clearenv()
+	defer SetEnv("BUILDKITE_TOKEN", "test")()
+
+	yaml := `
+ci:
+  buildkite:
+    organisation: example
+    token: abc
+vcs:
+  github:
+    organisation: example
+    token: abc
+`
+	file := filepath.Join(name, ".scaffold.yaml")
+	_ = ioutil.WriteFile(file, []byte(yaml), 0777)
+	defer func() { _ = os.Remove(file) }()
+
+	out := &bytes.Buffer{}
+
+	cfg, err := Load(name, out)
+	assert.NoError(t, err)
+	assert.NotNil(t, cfg)
+	assert.Equal(t, "test", cfg.CI.Buildkite.Token)
+}
+
+func TestLoad_SubDir_Overrides_Dir(t *testing.T) {
+	os.Clearenv()
+
+	yaml := `
+ci:
+  buildkite:
+    organisation: example
+    token: abc
+vcs:
+  github:
+    organisation: example
+    token: abc
+`
+	subYaml := `
+ci:
+  buildkite:
+    organisation: example
+    token: test
+vcs:
+  github:
+    organisation: example
+    token: abc
+`
+	file := filepath.Join(name, ".scaffold.yaml")
+	_ = ioutil.WriteFile(file, []byte(yaml), 0777)
+	defer func() { _ = os.Remove(file) }()
+	sub := filepath.Join(name, "sub")
+	_ = os.MkdirAll(sub, 0777)
+	defer func() { _ = os.RemoveAll(sub) }()
+	_ = ioutil.WriteFile(filepath.Join(sub, ".scaffold.yaml"), []byte(subYaml), 0777)
+
+	out := &bytes.Buffer{}
+
+	cfg, err := Load(sub, out)
+	assert.NoError(t, err)
+	assert.NotNil(t, cfg)
+	assert.Equal(t, "test", cfg.CI.Buildkite.Token)
+}
+
+func TestParseConfigFile_Return_Error_For_Unreadable_File(t *testing.T) {
+	out := &bytes.Buffer{}
+	dir := filepath.Join(name, ".scaffold.yaml")
+	_ = os.MkdirAll(dir, 0777)
+	defer func() { _ = os.RemoveAll(dir) }()
+
+	_, err := Load(name, out)
+	assert.EqualError(t, err, fmt.Sprintf("read %s: is a directory", dir))
+}
+
 func TestValidateConfig_No_VCS_Configured(t *testing.T) {
 	cfg := InitEmptyConfig()
 	err := cfg.ValidateConfig()
diff --git a/pkg/config/testing.go b/pkg/config/testing.go
new file mode 100644
index 0000000..b6ed25d
--- /dev/null
+++ b/pkg/config/testing.go
@@ -0,0 +1,12 @@
+// +build !prod
+
+package config
+
+import (
+	"os"
+)
+
+func SetEnv(key, value string) func() {
+	_ = os.Setenv(key, value)
+	return func() { _ = os.Unsetenv(key) }
+}
diff --git a/pkg/scaffold_test.go b/pkg/scaffold_test.go
index 61e2d1f..1fb5d26 100644
--- a/pkg/scaffold_test.go
+++ b/pkg/scaffold_test.go
@@ -102,6 +102,32 @@ vcs:
 	assert.Equal(t, fmt.Sprintf("\x1b[0mParsing config from file: \x1b[32m'%s'\x1b[39m\x1b[0m\n\x1b[0m\x1b[31mGET https://api.buildkite.com/v2/user: 401 Authentication required. Please supply a valid API Access Token: https://buildkite.com/docs/apis/rest-api#authentication\x1b[39m\x1b[0m\n", file), out.String())
 }
 
+func TestScaffold_Fails_For_Multiple_Configured_CIs(t *testing.T) {
+	defer SetEnv("GITLAB_GROUP", "test")()
+	defer SetEnv("GITLAB_TOKEN", "test")()
+
+	yaml := `
+ci:
+  buildkite:
+    organisation: example
+    token: abc
+vcs:
+  github:
+    organisation: example
+    token: abc
+`
+	file := filepath.Join(name, ".scaffold.yaml")
+	_ = ioutil.WriteFile(file, []byte(yaml), 0777)
+	defer func() { _ = os.Remove(file) }()
+
+	out := bytes.Buffer{}
+
+	exitCode := Setup(name, &out, "project")
+
+	assert.Equal(t, -3, exitCode)
+	assert.Equal(t, fmt.Sprintf("\x1b[0mParsing config from file: \x1b[32m'%s'\x1b[39m\x1b[0m\n\x1b[0m\x1b[31mscaffold CI already defined, please check configuration\x1b[39m\x1b[0m\n", file), out.String())
+}
+
 func TestScaffold_Configure_Error(t *testing.T) {
 	cfg := config.InitEmptyConfig()
 	cfg.CurrentCI = &mockCi{configErr: errors.New("config error")}