diff --git a/cmd/check.go b/cmd/check.go
index 9ccd1bd..2d906dd 100644
--- a/cmd/check.go
+++ b/cmd/check.go
@@ -50,7 +50,7 @@ func newCheckCommand() *cobra.Command {
 				return fmt.Errorf("resolve scan paths: %w", err)
 			}
 
-			engine, err := scanner.NewEngine(cfg, allow)
+			engine, err := scanner.NewEngineWithRoot(cfg, allow, repoRoot)
 			if err != nil {
 				return fmt.Errorf("create scanner: %w", err)
 			}
diff --git a/cmd/check_test.go b/cmd/check_test.go
index f1b0b4c..8692340 100644
--- a/cmd/check_test.go
+++ b/cmd/check_test.go
@@ -114,6 +114,43 @@ func TestCheckCommandExplicitMissingPathStillErrors(t *testing.T) {
 	assert.Contains(t, err.Error(), "stat path")
 }
 
+func TestCheckCommandFingerprintStableAcrossWorkingDirectories(t *testing.T) {
+	repoRoot := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(repoRoot, ".git", "hooks"), 0o755))
+	require.NoError(t, os.MkdirAll(filepath.Join(repoRoot, "nested"), 0o755))
+
+	target := filepath.Join(repoRoot, "secret.js")
+	require.NoError(t, os.WriteFile(target, []byte("const key = \"AKIA1234567890ABCDEF\";\n"), 0o644))
+
+	runCheck := func(t *testing.T, workdir string, arg string) scanner.Finding {
+		t.Helper()
+		chdirForTest(t, workdir)
+
+		cmd := newCheckCommand()
+		cmd.SilenceErrors = true
+		cmd.SilenceUsage = true
+		output := &bytes.Buffer{}
+		cmd.SetOut(output)
+		cmd.SetErr(io.Discard)
+		cmd.SetArgs([]string{arg, "--json"})
+
+		err := cmd.Execute()
+		require.ErrorIs(t, err, ErrFindings)
+
+		var findings []scanner.Finding
+		require.NoError(t, json.Unmarshal(output.Bytes(), &findings))
+		require.Len(t, findings, 1)
+		return findings[0]
+	}
+
+	rootFinding := runCheck(t, repoRoot, "secret.js")
+	nestedFinding := runCheck(t, filepath.Join(repoRoot, "nested"), "../secret.js")
+
+	assert.Equal(t, "secret.js", rootFinding.File)
+	assert.Equal(t, "secret.js", nestedFinding.File)
+	assert.Equal(t, rootFinding.Fingerprint, nestedFinding.Fingerprint)
+}
+
 func chdirForTest(t *testing.T, dir string) {
 	t.Helper()
 	wd, err := os.Getwd()
diff --git a/scanner/scanner.go b/scanner/scanner.go
index 30f0292..c1aba80 100644
--- a/scanner/scanner.go
+++ b/scanner/scanner.go
@@ -35,10 +35,16 @@ type Engine struct {
 	allow    allowlist.Set
 	patterns []PatternRule
 	warnings []string
+	rootDir  string
 }
 
 // NewEngine constructs a scanner engine.
 func NewEngine(cfg config.Config, allow allowlist.Set) (*Engine, error) {
+	return NewEngineWithRoot(cfg, allow, mustGetwd())
+}
+
+// NewEngineWithRoot constructs a scanner engine with a stable root directory for paths and fingerprints.
+func NewEngineWithRoot(cfg config.Config, allow allowlist.Set, rootDir string) (*Engine, error) {
 	patterns, err := AllPatterns(cfg)
 	if err != nil {
 		return nil, fmt.Errorf("build pattern set: %w", err)
@@ -46,7 +52,14 @@ func NewEngine(cfg config.Config, allow allowlist.Set) (*Engine, error) {
 	if allow == nil {
 		allow = allowlist.Set{}
 	}
-	return &Engine{cfg: cfg, allow: allow, patterns: patterns}, nil
+	if rootDir == "" {
+		rootDir = mustGetwd()
+	}
+	rootDir, err = filepath.Abs(rootDir)
+	if err != nil {
+		return nil, fmt.Errorf("resolve root dir %s: %w", rootDir, err)
+	}
+	return &Engine{cfg: cfg, allow: allow, patterns: patterns, rootDir: rootDir}, nil
 }
 
 // Warnings returns non-fatal scan warnings, such as skipped oversized files.
@@ -149,7 +162,7 @@ func (e *Engine) scanFile(path string) ([]Finding, error) {
 	}
 	defer file.Close()
 
-	relative, err := filepath.Rel(mustGetwd(), path)
+	relative, err := filepath.Rel(e.rootDir, path)
 	if err != nil {
 		relative = path
 	}