diff --git a/pkg/sbom/io/encode.go b/pkg/sbom/io/encode.go
index 64a24dbdcb07..096abd026b86 100644
--- a/pkg/sbom/io/encode.go
+++ b/pkg/sbom/io/encode.go
@@ -85,7 +85,8 @@ func (e *Encoder) rootComponent(r types.Report) (*core.Component, error) {
 		root.Type = core.TypeRepository
 	case artifact.TypeCycloneDX, artifact.TypeSPDX:
 		// When we scan SBOM file
-		if r.BOM != nil {
+		// If SBOM file doesn't contain root component - use filesystem
+		if r.BOM != nil && r.BOM.Root() != nil {
 			return r.BOM.Root(), nil
 		}
 		// When we scan a `json` file (meaning a file in `json` format) which was created from the SBOM file.
diff --git a/pkg/sbom/io/encode_test.go b/pkg/sbom/io/encode_test.go
index 06109c963d4f..80783827cee7 100644
--- a/pkg/sbom/io/encode_test.go
+++ b/pkg/sbom/io/encode_test.go
@@ -705,6 +705,53 @@ func TestEncoder_Encode(t *testing.T) {
 			},
 			wantVulns: make(map[uuid.UUID][]core.Vulnerability),
 		},
+		{
+			name: "SBOM file without root component",
+			report: types.Report{
+				SchemaVersion: 2,
+				ArtifactName:  "report.cdx.json",
+				ArtifactType:  artifact.TypeCycloneDX,
+				Results: []types.Result{
+					{
+						Target: "Java",
+						Type:   ftypes.Jar,
+						Class:  types.ClassLangPkg,
+						Packages: []ftypes.Package{
+							{
+								ID:      "org.apache.logging.log4j:log4j-core:2.23.1",
+								Name:    "org.apache.logging.log4j:log4j-core",
+								Version: "2.23.1",
+								Identifier: ftypes.PkgIdentifier{
+									UID: "6C0AE96901617503",
+									PURL: &packageurl.PackageURL{
+										Type:      packageurl.TypeMaven,
+										Namespace: "org.apache.logging.log4j",
+										Name:      "log4j-core",
+										Version:   "2.23.1",
+									},
+								},
+								FilePath: "log4j-core-2.23.1.jar",
+							},
+						},
+					},
+				},
+				BOM: newTestBOM2(t),
+			},
+			wantComponents: map[uuid.UUID]*core.Component{
+				uuid.MustParse("3ff14136-e09f-4df9-80ea-000000000001"): fsComponent,
+				uuid.MustParse("3ff14136-e09f-4df9-80ea-000000000002"): libComponent,
+			},
+			wantRels: map[uuid.UUID][]core.Relationship{
+				uuid.MustParse("3ff14136-e09f-4df9-80ea-000000000001"): {
+					{
+						Dependency: uuid.MustParse("3ff14136-e09f-4df9-80ea-000000000002"),
+						Type:       core.RelationshipContains,
+					},
+				},
+				uuid.MustParse("3ff14136-e09f-4df9-80ea-000000000002"): nil,
+			},
+			wantVulns: make(map[uuid.UUID][]core.Vulnerability),
+		},
 		{
 			name: "json file created from SBOM file (BOM is empty)",
 			report: types.Report{
@@ -860,3 +907,11 @@ func newTestBOM(t *testing.T) *core.BOM {
 	bom.AddComponent(appComponent)
 	return bom
 }
+
+// BOM without root component
+func newTestBOM2(t *testing.T) *core.BOM {
+	uuid.SetFakeUUID(t, "2ff14136-e09f-4df9-80ea-%012d")
+	bom := core.NewBOM(core.Options{})
+	bom.AddComponent(libComponent)
+	return bom
+}