diff --git a/internal/cli/admin.go b/internal/cli/admin.go
index 8047e867f..ef87a3415 100644
--- a/internal/cli/admin.go
+++ b/internal/cli/admin.go
@@ -862,6 +862,10 @@ func runPerRepoInstall(ctx context.Context, c perRepoInstallConfig) error {
 		// VendorBinary, UpstreamRef, UpstreamTag. Extra fields are included to stay aligned
 		// with the non-dry-run installCfg; Skip* flags are omitted because
 		// they control Install() flow, not scaffold file generation.
+		dryRunConfigLayout := repos.ConfigLayoutLayered
+		if alreadyInstalled {
+			dryRunConfigLayout = repos.ConfigLayoutUpgrade
+		}
 		dryRunFiles, dryRunErr := repos.BuildScaffoldFiles(repos.InstallConfig{
 			Owner:            owner,
 			Repo:             repo,
@@ -876,6 +880,7 @@ func runPerRepoInstall(ctx context.Context, c perRepoInstallConfig) error {
 			WIFProvider:      inferenceWIFProvider,
 			VendorBinary:     vendor,
 			Direct:           c.Direct,
+			ConfigLayout:     dryRunConfigLayout,
 		})
 		if dryRunErr != nil {
 			return fmt.Errorf("generating scaffold files for dry run: %w", dryRunErr)
@@ -1084,6 +1089,11 @@ func runPerRepoInstall(ctx context.Context, c perRepoInstallConfig) error {
 	// Resolve review app client ID for provenance validation.
 	reviewAppClientID := resolveReviewAppClientID(ctx, client, c.AppSet)
 
+	configLayout := repos.ConfigLayoutLayered
+	if alreadyInstalled {
+		configLayout = repos.ConfigLayoutUpgrade
+	}
+
 	installCfg := repos.InstallConfig{
 		Owner:                 owner,
 		Repo:                  repo,
@@ -1101,6 +1111,7 @@ func runPerRepoInstall(ctx context.Context, c perRepoInstallConfig) error {
 		VendorBinary:          vendor,
 		Direct:                c.Direct,
 		SkipScaffoldAndConfig: vendor,
+		ConfigLayout:          configLayout,
 	}
 
 	progressFn := func(_ string, phase, msg string) {
diff --git a/internal/cli/admin_test.go b/internal/cli/admin_test.go
index 6af1a00d5..571393695 100644
--- a/internal/cli/admin_test.go
+++ b/internal/cli/admin_test.go
@@ -2280,6 +2280,75 @@ func TestRunPerRepoInstall_AlreadyInstalledUpgrade(t *testing.T) {
 	require.NoError(t, err)
 }
 
+// TestRunPerRepoInstall_FreshInstall_LayeredConfig verifies that a fresh
+// per-repo install generates both config.base.yaml (scaffold defaults)
+// and config.yaml (minimal overlay) per the layered config model.
+func TestRunPerRepoInstall_FreshInstall_LayeredConfig(t *testing.T) {
+	client := forge.NewFakeClient()
+	client.Repos = []forge.Repository{
+		{Name: "widget", FullName: "acme/widget", DefaultBranch: "main"},
+	}
+
+	cfg := perRepoTestBase()
+	cfg.testClient = client
+	cfg.Direct = true
+
+	err := runPerRepoInstall(context.Background(), cfg)
+	require.NoError(t, err)
+
+	// Verify scaffold files include both config.base.yaml and config.yaml.
+	require.NotEmpty(t, client.CommittedFiles, "expected scaffold files to be committed")
+	paths := make(map[string]string)
+	for _, f := range client.CommittedFiles[0].Files {
+		paths[f.Path] = string(f.Content)
+	}
+
+	assert.Contains(t, paths, ".fullsend/config.base.yaml",
+		"fresh install should generate config.base.yaml")
+	assert.Contains(t, paths, ".fullsend/config.yaml",
+		"fresh install should generate config.yaml overlay")
+
+	// config.base.yaml should contain scaffold defaults (roles).
+	assert.Contains(t, paths[".fullsend/config.base.yaml"], "roles:",
+		"config.base.yaml should contain roles")
+
+	// config.yaml should be a minimal overlay (no roles baked in).
+	assert.NotContains(t, paths[".fullsend/config.yaml"], "roles:",
+		"config.yaml overlay should not contain roles")
+}
+
+// TestRunPerRepoInstall_ReOnboarding_PreservesUserConfig verifies that
+// re-onboarding generates config.base.yaml with new defaults but does
+// NOT overwrite config.yaml (the user-owned overlay).
+func TestRunPerRepoInstall_ReOnboarding_PreservesUserConfig(t *testing.T) {
+	client := forge.NewFakeClient()
+	client.VariableValues = map[string]string{
+		"acme/widget/FULLSEND_MINT_URL": "https://mint.example.com/v1/token",
+	}
+	client.Repos = []forge.Repository{
+		{Name: "widget", FullName: "acme/widget", DefaultBranch: "main"},
+	}
+
+	cfg := perRepoTestBase()
+	cfg.testClient = client
+	cfg.Direct = true
+
+	err := runPerRepoInstall(context.Background(), cfg)
+	require.NoError(t, err)
+
+	// Verify scaffold files include config.base.yaml but NOT config.yaml.
+	require.NotEmpty(t, client.CommittedFiles, "expected scaffold files to be committed")
+	paths := make(map[string]bool)
+	for _, f := range client.CommittedFiles[0].Files {
+		paths[f.Path] = true
+	}
+
+	assert.True(t, paths[".fullsend/config.base.yaml"],
+		"re-onboarding should generate config.base.yaml")
+	assert.False(t, paths[".fullsend/config.yaml"],
+		"re-onboarding should NOT overwrite config.yaml — it is user-owned")
+}
+
 func TestRunPerRepoInstall_DryRun(t *testing.T) {
 	client := forge.NewFakeClient()
 
diff --git a/internal/repos/install.go b/internal/repos/install.go
index f94e6380f..2977ee3c0 100644
--- a/internal/repos/install.go
+++ b/internal/repos/install.go
@@ -24,6 +24,44 @@ var WIFProviderPattern = regexp.MustCompile(
 	`^projects/\d+/locations/global/workloadIdentityPools/[a-z][a-z0-9-]{2,30}[a-z0-9]/providers/[a-z][a-z0-9-]{2,30}[a-z0-9]$`,
 )
 
+// ConfigLayout controls how BuildScaffoldFiles generates per-repo config
+// files. The default (empty string) preserves backward-compatible behavior.
+type ConfigLayout string
+
+const (
+	// ConfigLayoutDefault generates .fullsend/config.yaml with full
+	// scaffold defaults baked in. This is the backward-compatible default
+	// used by callers that have not opted into the layered config model
+	// (e.g. converge/drift detection).
+	ConfigLayoutDefault ConfigLayout = ""
+
+	// ConfigLayoutLayered generates .fullsend/config.base.yaml with
+	// scaffold defaults and .fullsend/config.yaml as a minimal user-owned
+	// overlay. Used for fresh installs via admin install.
+	ConfigLayoutLayered ConfigLayout = "layered"
+
+	// ConfigLayoutUpgrade generates only .fullsend/config.base.yaml with
+	// scaffold defaults. config.yaml is user-owned and left untouched.
+	// Used for re-onboarding via admin install.
+	ConfigLayoutUpgrade ConfigLayout = "upgrade"
+)
+
+// minimalOverlayYAML is the stub config.yaml overlay committed on fresh
+// installs when ConfigLayoutLayered is active. Scaffold defaults live in
+// config.base.yaml; this file is user-owned for customization.
+const minimalOverlayYAML = `# fullsend per-repo configuration (overlay)
+# https://github.com/fullsend-ai/fullsend
+#
+# This file is the per-repo overlay for fullsend configuration.
+# Scaffold defaults are provided by config.base.yaml.
+# Values set here override the base layer. Omitted fields inherit
+# from config.base.yaml, then from compiled-in code defaults.
+#
+# See https://fullsend.sh/docs/guides/infrastructure/layered-config-reference
+
+version: "1"
+`
+
 // InstallConfig is a pure data struct holding all inputs needed for a
 // per-repo installation. CLI flags, environment variables, and interactive
 // prompts are resolved by the caller before constructing this struct.
@@ -83,6 +121,10 @@ type InstallConfig struct {
 	// pipeline YAML so that agent jobs are routed to specific runners.
 	RunnerTags []string
 
+	// ConfigLayout controls how BuildScaffoldFiles generates per-repo
+	// config files. See the ConfigLayout* constants.
+	ConfigLayout ConfigLayout
+
 	// Direct controls scaffold delivery: true pushes directly to the default
 	// branch; false creates a PR.
 	Direct bool
@@ -402,11 +444,49 @@ func BuildScaffoldFiles(cfg InstallConfig) ([]forge.TreeFile, error) {
 			Mode:    f.Mode,
 		})
 	}
-	files = append(files, forge.TreeFile{
-		Path:    ".fullsend/config.yaml",
-		Content: cfgYAML,
-		Mode:    "100644",
-	})
+
+	// When PerRepoConfig is set, the caller provided an explicit config
+	// (e.g. migration path). Always write it as config.yaml regardless
+	// of ConfigLayout. When PerRepoConfig is nil, ConfigLayout controls
+	// the file strategy.
+	if cfg.PerRepoConfig != nil {
+		files = append(files, forge.TreeFile{
+			Path:    ".fullsend/config.yaml",
+			Content: cfgYAML,
+			Mode:    "100644",
+		})
+	} else {
+		switch cfg.ConfigLayout {
+		case ConfigLayoutLayered:
+			// Fresh install with layered config: write scaffold defaults
+			// to config.base.yaml and a minimal overlay to config.yaml.
+			files = append(files, forge.TreeFile{
+				Path:    ".fullsend/config.base.yaml",
+				Content: cfgYAML,
+				Mode:    "100644",
+			})
+			files = append(files, forge.TreeFile{
+				Path:    ".fullsend/config.yaml",
+				Content: []byte(minimalOverlayYAML),
+				Mode:    "100644",
+			})
+		case ConfigLayoutUpgrade:
+			// Re-onboarding: regenerate config.base.yaml with new
+			// defaults. config.yaml is user-owned and left untouched.
+			files = append(files, forge.TreeFile{
+				Path:    ".fullsend/config.base.yaml",
+				Content: cfgYAML,
+				Mode:    "100644",
+			})
+		default:
+			// Legacy/default: single config.yaml with full defaults.
+			files = append(files, forge.TreeFile{
+				Path:    ".fullsend/config.yaml",
+				Content: cfgYAML,
+				Mode:    "100644",
+			})
+		}
+	}
 
 	return files, nil
 }
diff --git a/internal/repos/install_test.go b/internal/repos/install_test.go
index cb05794d6..fce2c52c3 100644
--- a/internal/repos/install_test.go
+++ b/internal/repos/install_test.go
@@ -7,6 +7,7 @@ import (
 	"sync"
 	"testing"
 
+	"github.com/fullsend-ai/fullsend/internal/config"
 	"github.com/fullsend-ai/fullsend/internal/forge"
 	"github.com/fullsend-ai/fullsend/internal/scaffold"
 )
@@ -898,6 +899,160 @@ func TestBuildScaffoldFiles_UnsupportedForge(t *testing.T) {
 	}
 }
 
+// TestBuildScaffoldFiles_LayeredFreshInstall verifies that a fresh install
+// with ConfigLayoutLayered generates both config.base.yaml (scaffold
+// defaults) and config.yaml (minimal overlay).
+func TestBuildScaffoldFiles_LayeredFreshInstall(t *testing.T) {
+	cfg := baseCfg()
+	cfg.ConfigLayout = ConfigLayoutLayered
+
+	files, err := BuildScaffoldFiles(cfg)
+	if err != nil {
+		t.Fatalf("BuildScaffoldFiles() returned error: %v", err)
+	}
+
+	paths := make(map[string][]byte)
+	for _, f := range files {
+		paths[f.Path] = f.Content
+	}
+
+	// config.base.yaml must exist with scaffold defaults.
+	baseContent, hasBase := paths[".fullsend/config.base.yaml"]
+	if !hasBase {
+		t.Fatal("expected .fullsend/config.base.yaml in scaffold files")
+	}
+	if !strings.Contains(string(baseContent), "roles:") {
+		t.Error("config.base.yaml should contain roles")
+	}
+
+	// config.yaml must exist as a minimal overlay.
+	overlayContent, hasOverlay := paths[".fullsend/config.yaml"]
+	if !hasOverlay {
+		t.Fatal("expected .fullsend/config.yaml in scaffold files")
+	}
+	if !strings.Contains(string(overlayContent), "version:") {
+		t.Error("config.yaml overlay should contain version")
+	}
+	// The overlay must NOT contain scaffold defaults like roles.
+	if strings.Contains(string(overlayContent), "roles:") {
+		t.Error("config.yaml overlay should not contain roles (those belong in config.base.yaml)")
+	}
+}
+
+// TestBuildScaffoldFiles_UpgradeSkipsConfigYAML verifies that re-onboarding
+// with ConfigLayoutUpgrade generates config.base.yaml but does NOT generate
+// config.yaml, leaving the user's existing overlay untouched.
+func TestBuildScaffoldFiles_UpgradeSkipsConfigYAML(t *testing.T) {
+	cfg := baseCfg()
+	cfg.ConfigLayout = ConfigLayoutUpgrade
+
+	files, err := BuildScaffoldFiles(cfg)
+	if err != nil {
+		t.Fatalf("BuildScaffoldFiles() returned error: %v", err)
+	}
+
+	var hasBase, hasConfig bool
+	for _, f := range files {
+		switch f.Path {
+		case ".fullsend/config.base.yaml":
+			hasBase = true
+			if !strings.Contains(string(f.Content), "roles:") {
+				t.Error("config.base.yaml should contain roles")
+			}
+		case ".fullsend/config.yaml":
+			hasConfig = true
+		}
+	}
+	if !hasBase {
+		t.Fatal("expected .fullsend/config.base.yaml in scaffold files")
+	}
+	if hasConfig {
+		t.Error("config.yaml should NOT be generated on upgrade — it is user-owned")
+	}
+}
+
+// TestBuildScaffoldFiles_UpgradeRuntime verifies that --runtime on
+// re-onboarding writes the runtime to config.base.yaml.
+func TestBuildScaffoldFiles_UpgradeRuntime(t *testing.T) {
+	cfg := baseCfg()
+	cfg.ConfigLayout = ConfigLayoutUpgrade
+	cfg.Runtime = "pi"
+
+	files, err := BuildScaffoldFiles(cfg)
+	if err != nil {
+		t.Fatalf("BuildScaffoldFiles() returned error: %v", err)
+	}
+
+	for _, f := range files {
+		if f.Path == ".fullsend/config.base.yaml" {
+			if !strings.Contains(string(f.Content), "runtime: pi") {
+				t.Errorf("config.base.yaml should contain runtime: pi:\n%s", f.Content)
+			}
+			return
+		}
+	}
+	t.Fatal("expected .fullsend/config.base.yaml in scaffold files")
+}
+
+// TestBuildScaffoldFiles_DefaultLayoutBackwardCompat verifies that the
+// default ConfigLayout (empty string) preserves backward-compatible
+// behavior: a single config.yaml with full defaults, no config.base.yaml.
+func TestBuildScaffoldFiles_DefaultLayoutBackwardCompat(t *testing.T) {
+	cfg := baseCfg()
+	// ConfigLayout is zero value (ConfigLayoutDefault).
+
+	files, err := BuildScaffoldFiles(cfg)
+	if err != nil {
+		t.Fatalf("BuildScaffoldFiles() returned error: %v", err)
+	}
+
+	var hasConfig, hasBase bool
+	for _, f := range files {
+		switch f.Path {
+		case ".fullsend/config.yaml":
+			hasConfig = true
+		case ".fullsend/config.base.yaml":
+			hasBase = true
+		}
+	}
+	if !hasConfig {
+		t.Error("expected .fullsend/config.yaml with default layout")
+	}
+	if hasBase {
+		t.Error("config.base.yaml should NOT be generated with default layout")
+	}
+}
+
+// TestBuildScaffoldFiles_PerRepoConfigOverrideIgnoresLayout verifies that
+// when PerRepoConfig is set (migration/override path), ConfigLayout is
+// ignored and config.yaml is generated from the provided config.
+func TestBuildScaffoldFiles_PerRepoConfigOverrideIgnoresLayout(t *testing.T) {
+	cfg := baseCfg()
+	cfg.ConfigLayout = ConfigLayoutUpgrade
+	cfg.PerRepoConfig = config.NewPerRepoConfig([]string{"triage"}, "acme/widgets")
+
+	files, err := BuildScaffoldFiles(cfg)
+	if err != nil {
+		t.Fatalf("BuildScaffoldFiles() returned error: %v", err)
+	}
+
+	var hasConfig, hasBase bool
+	for _, f := range files {
+		switch f.Path {
+		case ".fullsend/config.yaml":
+			hasConfig = true
+		case ".fullsend/config.base.yaml":
+			hasBase = true
+		}
+	}
+	if !hasConfig {
+		t.Error("expected .fullsend/config.yaml when PerRepoConfig is set")
+	}
+	if hasBase {
+		t.Error("config.base.yaml should NOT be generated when PerRepoConfig is set")
+	}
+}
+
 func TestInstall_FreshInstall_GitLab(t *testing.T) {
 	fc := newFakeClientWithRepo()
 	cfg := InstallConfig{