diff --git a/pkg/analysis/passes/gomanifest/gomanifest.go b/pkg/analysis/passes/gomanifest/gomanifest.go
index 99cf1cea..3ae2bfd8 100644
--- a/pkg/analysis/passes/gomanifest/gomanifest.go
+++ b/pkg/analysis/passes/gomanifest/gomanifest.go
@@ -9,7 +9,6 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
-	"slices"
 	"strings"
 
 	"github.com/bmatcuk/doublestar/v4"
@@ -73,6 +72,11 @@ func run(pass *analysis.Pass) (interface{}, error) {
 		return nil, nil
 	}
 
+	goFiles, err = filterPluginGoFiles(sourceCodeDir, goFiles)
+	if err != nil {
+		return nil, err
+	}
+
 	if len(goFiles) == 0 {
 		// no go files found so we can't check the manifest
 		return nil, nil
@@ -159,9 +163,8 @@ func parseManifestFile(file string) (map[string]string, error) {
 		}
 		sha256sum := strings.TrimSpace(parsedLine[0])
 		fileName := normalizeFileName(strings.TrimSpace(parsedLine[1]))
-		// skip known non-backend files that some published plugins
-		// include in their manifest
-		if slices.Contains(ignoredManifestFiles, fileName) {
+		// skip non-plugin files that may exist in dependency folders
+		if isNodeModulesPath(fileName) {
 			continue
 		}
 		// format the manifest fileName:sha256sum
@@ -175,18 +178,37 @@ func parseManifestFile(file string) (map[string]string, error) {
 	return manifest, nil
 }
 
-// ignoredManifestFiles lists specific files that should be ignored when
-// validating the manifest. These are files that some published plugins
-// include in their manifest but are not part of the backend source code.
-var ignoredManifestFiles = []string{
-	"node_modules/flatted/golang/pkg/flatted/flatted.go",
-}
-
 func normalizeFileName(fileName string) string {
 	// takes a filename that might have windows or linux separators and converts them to a linux separator
 	return strings.Replace(fileName, "\\", "/", -1)
 }
 
+func isNodeModulesPath(fileName string) bool {
+	normalized := normalizeFileName(fileName)
+	return normalized == "node_modules" ||
+		strings.HasPrefix(normalized, "node_modules/") ||
+		strings.Contains(normalized, "/node_modules/")
+}
+
+func filterPluginGoFiles(sourceCodeDir string, goFiles []string) ([]string, error) {
+	filteredGoFiles := make([]string, 0, len(goFiles))
+
+	for _, goFilePath := range goFiles {
+		goFileRelativePath, err := filepath.Rel(sourceCodeDir, goFilePath)
+		if err != nil {
+			return nil, err
+		}
+
+		if isNodeModulesPath(goFileRelativePath) {
+			continue
+		}
+
+		filteredGoFiles = append(filteredGoFiles, goFilePath)
+	}
+
+	return filteredGoFiles, nil
+}
+
 func verifyManifest(
 	manifest map[string]string,
 	goFiles []string,
diff --git a/pkg/analysis/passes/gomanifest/gomanifest_test.go b/pkg/analysis/passes/gomanifest/gomanifest_test.go
index 93d9f967..9d9f4e9c 100644
--- a/pkg/analysis/passes/gomanifest/gomanifest_test.go
+++ b/pkg/analysis/passes/gomanifest/gomanifest_test.go
@@ -218,3 +218,41 @@ func TestWindowsLineEndingsManifest(t *testing.T) {
 	prettyprint.Print(interceptor.Diagnostics)
 	require.Len(t, interceptor.Diagnostics, 0)
 }
+
+func TestIsNodeModulesPath(t *testing.T) {
+	testCases := []struct {
+		name     string
+		path     string
+		expected bool
+	}{
+		{name: "exact node_modules", path: "node_modules", expected: true},
+		{name: "root node_modules child", path: "node_modules/flatted/main.go", expected: true},
+		{name: "nested node_modules child", path: "src/node_modules/flatted/main.go", expected: true},
+		{name: "windows separators", path: `src\\node_modules\\flatted\\main.go`, expected: true},
+		{name: "similar but different directory name", path: "node_modules2/flatted/main.go", expected: false},
+		{name: "regular source path", path: "pkg/main.go", expected: false},
+	}
+
+	for _, tc := range testCases {
+		t.Run(tc.name, func(t *testing.T) {
+			require.Equal(t, tc.expected, isNodeModulesPath(tc.path))
+		})
+	}
+}
+
+func TestFilterPluginGoFiles(t *testing.T) {
+	sourceCodeDir := filepath.Join("repo", "plugin")
+	goFiles := []string{
+		filepath.Join(sourceCodeDir, "pkg", "main.go"),
+		filepath.Join(sourceCodeDir, "pkg", "subdir", "worker.go"),
+		filepath.Join(sourceCodeDir, "node_modules", "flatted", "main.go"),
+		filepath.Join(sourceCodeDir, "src", "node_modules", "dep", "dep.go"),
+	}
+
+	filtered, err := filterPluginGoFiles(sourceCodeDir, goFiles)
+	require.NoError(t, err)
+	require.Equal(t, []string{
+		filepath.Join(sourceCodeDir, "pkg", "main.go"),
+		filepath.Join(sourceCodeDir, "pkg", "subdir", "worker.go"),
+	}, filtered)
+}