diff --git a/internal/cli/diff.go b/internal/cli/diff.go
index 3866096..b5c781a 100644
--- a/internal/cli/diff.go
+++ b/internal/cli/diff.go
@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"os"
 
+	"github.com/glincker/stacklit/internal/config"
 	"github.com/glincker/stacklit/internal/git"
 	"github.com/glincker/stacklit/internal/schema"
 	"github.com/glincker/stacklit/internal/walker"
@@ -32,8 +33,9 @@ func newDiffCmd() *cobra.Command {
 				return fmt.Errorf("stacklit.json has no merkle_hash; run 'stacklit generate' to rebuild")
 			}
 
-			// 2. Walk current source files
-			files, err := walker.Walk(".", nil)
+			// 2. Walk current source files, excluding Stacklit's own generated outputs.
+			cfg := config.Load(".")
+			files, err := walker.Walk(".", cfg.ScanIgnore())
 			if err != nil {
 				return fmt.Errorf("failed to walk source files: %w", err)
 			}
diff --git a/internal/config/config.go b/internal/config/config.go
index e32b340..3237864 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -72,3 +72,16 @@ func Load(root string) *Config {
 
 	return cfg
 }
+
+// ScanIgnore returns ignore patterns plus Stacklit output files so generated artifacts
+// never feed back into the next scan.
+func (c *Config) ScanIgnore() []string {
+	ignore := append([]string{}, c.Ignore...)
+	for _, out := range []string{c.Output.JSON, c.Output.Mermaid, c.Output.HTML} {
+		if out == "" {
+			continue
+		}
+		ignore = append(ignore, filepath.ToSlash(out))
+	}
+	return ignore
+}
diff --git a/internal/config/config_test.go b/internal/config/config_test.go
index 84ee17d..d242615 100644
--- a/internal/config/config_test.go
+++ b/internal/config/config_test.go
@@ -54,3 +54,22 @@ func TestLoadMalformed(t *testing.T) {
 		t.Errorf("expected default max_depth=4 after malformed file, got %d", cfg.MaxDepth)
 	}
 }
+
+func TestScanIgnoreIncludesOutputs(t *testing.T) {
+	cfg := DefaultConfig()
+	cfg.Ignore = []string{"custom/"}
+	cfg.Output.JSON = "out\\stacklit.json"
+	cfg.Output.Mermaid = "docs\\DEPENDENCIES.md"
+	cfg.Output.HTML = "stacklit.html"
+
+	got := cfg.ScanIgnore()
+	want := []string{"custom/", "out/stacklit.json", "docs/DEPENDENCIES.md", "stacklit.html"}
+	if len(got) != len(want) {
+		t.Fatalf("expected %d ignore patterns, got %d: %v", len(want), len(got), got)
+	}
+	for i := range want {
+		if got[i] != want[i] {
+			t.Fatalf("expected ignore[%d]=%q, got %q (all=%v)", i, want[i], got[i], got)
+		}
+	}
+}
diff --git a/internal/engine/engine.go b/internal/engine/engine.go
index a6ec071..6cfee88 100644
--- a/internal/engine/engine.go
+++ b/internal/engine/engine.go
@@ -166,7 +166,7 @@ func Run(opts Options) (*Result, error) {
 	}
 
 	// 3. Walk the filesystem, honouring extra ignore patterns from config.
-	files, err := walker.Walk(root, cfg.Ignore)
+	files, err := walker.Walk(root, cfg.ScanIgnore())
 	if err != nil {
 		return nil, fmt.Errorf("walking %s: %w", root, err)
 	}
diff --git a/internal/walker/walker.go b/internal/walker/walker.go
index ef1e193..229266c 100644
--- a/internal/walker/walker.go
+++ b/internal/walker/walker.go
@@ -99,6 +99,9 @@ func Walk(root string, extraIgnore []string) ([]string, error) {
 			return relErr
 		}
 
+		// Normalize path separators so generated output and ignore matching stay stable across OSes.
+		rel = filepath.ToSlash(rel)
+
 		// Skip the root itself.
 		if rel == "." {
 			return nil
diff --git a/internal/walker/walker_test.go b/internal/walker/walker_test.go
index 17d062f..35115ca 100644
--- a/internal/walker/walker_test.go
+++ b/internal/walker/walker_test.go
@@ -35,8 +35,8 @@ func TestWalkSourceFiles(t *testing.T) {
 	// Must include Go source files.
 	wantIncluded := []string{
 		"main.go",
-		filepath.Join("internal", "handler.go"),
-		filepath.Join("internal", "handler_test.go"),
+		filepath.ToSlash(filepath.Join("internal", "handler.go")),
+		filepath.ToSlash(filepath.Join("internal", "handler_test.go")),
 	}
 	for _, want := range wantIncluded {
 		if !fileSet[want] {
@@ -46,8 +46,8 @@ func TestWalkSourceFiles(t *testing.T) {
 
 	// Must exclude gitignored directories.
 	wantExcluded := []string{
-		filepath.Join("vendor", "lib.go"),
-		filepath.Join("node_modules", "pkg.js"),
+		filepath.ToSlash(filepath.Join("vendor", "lib.go")),
+		filepath.ToSlash(filepath.Join("node_modules", "pkg.js")),
 	}
 	for _, exclude := range wantExcluded {
 		if fileSet[exclude] {
@@ -124,7 +124,7 @@ func TestWalkAlwaysIgnoresDirs(t *testing.T) {
 	}
 
 	for _, d := range ignoredDirs {
-		p := filepath.Join(d, "file.go")
+		p := filepath.ToSlash(filepath.Join(d, "file.go"))
 		if fileSet[p] {
 			t.Errorf("expected %q inside always-ignore dir to be excluded", p)
 		}