diff --git a/pkg/fanal/analyzer/sbom/sbom.go b/pkg/fanal/analyzer/sbom/sbom.go
index 55768cff3a9b..20a069d52961 100644
--- a/pkg/fanal/analyzer/sbom/sbom.go
+++ b/pkg/fanal/analyzer/sbom/sbom.go
@@ -4,6 +4,7 @@ import (
 	"context"
 	"os"
 	"path"
+	"slices"
 	"strings"
 
 	"golang.org/x/xerrors"
@@ -51,6 +52,14 @@ func (a sbomAnalyzer) Analyze(ctx context.Context, input analyzer.AnalysisInput)
 		handleBitnamiImages(path.Dir(input.FilePath), bom)
 	}
 
+	// FilePath for apps with aggregatingTypes is empty.
+	// Set the SBOM file path as Application.FilePath to correctly overwrite applications when merging layers.
+	for i, app := range bom.Applications {
+		if slices.Contains(ftypes.AggregatingTypes, app.Type) && app.FilePath == "" {
+			bom.Applications[i].FilePath = input.FilePath
+		}
+	}
+
 	return &analyzer.AnalysisResult{
 		PackageInfos: bom.Packages,
 		Applications: bom.Applications,
diff --git a/pkg/fanal/analyzer/sbom/sbom_test.go b/pkg/fanal/analyzer/sbom/sbom_test.go
index 542a7f50addd..3e0f252b17d7 100644
--- a/pkg/fanal/analyzer/sbom/sbom_test.go
+++ b/pkg/fanal/analyzer/sbom/sbom_test.go
@@ -28,7 +28,34 @@ func Test_sbomAnalyzer_Analyze(t *testing.T) {
 			want: &analyzer.AnalysisResult{
 				Applications: []types.Application{
 					{
-						Type: types.Jar,
+						Type:     types.Bitnami,
+						FilePath: "opt/bitnami/elasticsearch",
+						Packages: types.Packages{
+							{
+								ID:       "elasticsearch@8.9.1",
+								Name:     "elasticsearch",
+								Version:  "8.9.1",
+								Arch:     "arm64",
+								Licenses: []string{"Elastic-2.0"},
+								Identifier: types.PkgIdentifier{
+									PURL: &packageurl.PackageURL{
+										Type:    packageurl.TypeBitnami,
+										Name:    "elasticsearch",
+										Version: "8.9.1",
+										Qualifiers: packageurl.Qualifiers{
+											{
+												Key:   "arch",
+												Value: "arm64",
+											},
+										},
+									},
+								},
+							},
+						},
+					},
+					{
+						Type:     types.Jar,
+						FilePath: "opt/bitnami/elasticsearch/.spdx-elasticsearch.spdx",
 						Packages: types.Packages{
 							{
 								ID:       "co.elastic.apm:apm-agent:1.36.0",
@@ -88,32 +115,6 @@ func Test_sbomAnalyzer_Analyze(t *testing.T) {
 							},
 						},
 					},
-					{
-						Type:     types.Bitnami,
-						FilePath: "opt/bitnami/elasticsearch",
-						Packages: types.Packages{
-							{
-								ID:       "elasticsearch@8.9.1",
-								Name:     "elasticsearch",
-								Version:  "8.9.1",
-								Arch:     "arm64",
-								Licenses: []string{"Elastic-2.0"},
-								Identifier: types.PkgIdentifier{
-									PURL: &packageurl.PackageURL{
-										Type:    packageurl.TypeBitnami,
-										Name:    "elasticsearch",
-										Version: "8.9.1",
-										Qualifiers: packageurl.Qualifiers{
-											{
-												Key:   "arch",
-												Value: "arm64",
-											},
-										},
-									},
-								},
-							},
-						},
-					},
 				},
 			},
 			wantErr: require.NoError,
@@ -125,7 +126,8 @@ func Test_sbomAnalyzer_Analyze(t *testing.T) {
 			want: &analyzer.AnalysisResult{
 				Applications: []types.Application{
 					{
-						Type: types.Jar,
+						Type:     types.Jar,
+						FilePath: "opt/bitnami/elasticsearch/.spdx-elasticsearch.cdx",
 						Packages: types.Packages{
 							{
 								FilePath: "opt/bitnami/elasticsearch/modules/apm/elastic-apm-agent-1.36.0.jar",