diff --git a/pkg/sbom/cyclonedx/marshal.go b/pkg/sbom/cyclonedx/marshal.go
index 75dd2db93b..785d4fc405 100644
--- a/pkg/sbom/cyclonedx/marshal.go
+++ b/pkg/sbom/cyclonedx/marshal.go
@@ -56,8 +56,7 @@ func NewMarshaler(version string) Marshaler {
 // MarshalReport converts the Trivy report to the CycloneDX format
 func (m *Marshaler) MarshalReport(ctx context.Context, report types.Report) (*cdx.BOM, error) {
 	// Convert into an intermediate representation
-	opts := core.Options{GenerateBOMRef: true}
-	bom, err := sbomio.NewEncoder(opts).Encode(report)
+	bom, err := sbomio.NewEncoder(sbomio.WithBOMRef()).Encode(report)
 	if err != nil {
 		return nil, xerrors.Errorf("failed to marshal report: %w", err)
 	}
diff --git a/pkg/sbom/io/encode.go b/pkg/sbom/io/encode.go
index dfaca17d06..1cdc77f170 100644
--- a/pkg/sbom/io/encode.go
+++ b/pkg/sbom/io/encode.go
@@ -19,21 +19,49 @@ import (
 	"github.com/aquasecurity/trivy/pkg/types"
 )
 
-type Encoder struct {
-	bom  *core.BOM
-	opts core.Options
+type EncoderOption func(*Encoder)
+
+// WithBOMRef enables BOM-Ref generation for CycloneDX components
+func WithBOMRef() EncoderOption {
+	return func(e *Encoder) {
+		e.bomOpts.GenerateBOMRef = true
+	}
 }
 
-func NewEncoder(opts core.Options) *Encoder {
-	return &Encoder{opts: opts}
+// WithParents enables holding parent maps in the BOM structure
+func WithParents() EncoderOption {
+	return func(e *Encoder) {
+		e.bomOpts.Parents = true
+	}
+}
+
+// ForceRegenerate forces regeneration of BOM instead of reusing existing one
+func ForceRegenerate() EncoderOption {
+	return func(e *Encoder) {
+		e.forceRegenerate = true
+	}
+}
+
+type Encoder struct {
+	bom             *core.BOM
+	bomOpts         core.Options
+	forceRegenerate bool
+}
+
+func NewEncoder(opts ...EncoderOption) *Encoder {
+	e := &Encoder{}
+	for _, opt := range opts {
+		opt(e)
+	}
+	return e
 }
 
 func (e *Encoder) Encode(report types.Report) (*core.BOM, error) {
-	// When report.BOM is not nil, reuse the existing BOM structure.
+	// When report.BOM is not nil, reuse the existing BOM structure unless ForceRegenerate is set.
 	// This happens in two scenarios:
 	// 1. SBOM scanning: When scanning an existing SBOM file to refresh vulnerabilities
 	// 2. Library usage: When using Trivy as a library with a custom BOM in the report
-	if report.BOM != nil {
+	if report.BOM != nil && !e.forceRegenerate {
 		return e.reuseExistingBOM(report)
 	}
 	// Metadata component
@@ -42,7 +70,7 @@ func (e *Encoder) Encode(report types.Report) (*core.BOM, error) {
 		return nil, xerrors.Errorf("failed to create root component: %w", err)
 	}
 
-	e.bom = core.NewBOM(e.opts)
+	e.bom = core.NewBOM(e.bomOpts)
 	if report.BOM != nil {
 		e.bom.SerialNumber = report.BOM.SerialNumber
 		e.bom.Version = report.BOM.Version
diff --git a/pkg/sbom/io/encode_test.go b/pkg/sbom/io/encode_test.go
index 2d67f29c4c..e64d6960d7 100644
--- a/pkg/sbom/io/encode_test.go
+++ b/pkg/sbom/io/encode_test.go
@@ -1466,8 +1466,7 @@ func TestEncoder_Encode(t *testing.T) {
 		t.Run(tt.name, func(t *testing.T) {
 			uuid.SetFakeUUID(t, "3ff14136-e09f-4df9-80ea-%012d")
 
-			opts := core.Options{GenerateBOMRef: true}
-			got, err := sbomio.NewEncoder(opts).Encode(tt.report)
+			got, err := sbomio.NewEncoder(sbomio.WithBOMRef()).Encode(tt.report)
 			if tt.wantErr != "" {
 				require.ErrorContains(t, err, tt.wantErr)
 				return
diff --git a/pkg/sbom/spdx/marshal.go b/pkg/sbom/spdx/marshal.go
index 3af2fbb80e..dad1d7ca4e 100644
--- a/pkg/sbom/spdx/marshal.go
+++ b/pkg/sbom/spdx/marshal.go
@@ -115,7 +115,7 @@ func NewMarshaler(version string, opts ...marshalOption) *Marshaler {
 
 func (m *Marshaler) MarshalReport(ctx context.Context, report types.Report) (*spdx.Document, error) {
 	// Convert into an intermediate representation
-	bom, err := sbomio.NewEncoder(core.Options{}).Encode(report)
+	bom, err := sbomio.NewEncoder().Encode(report)
 	if err != nil {
 		return nil, xerrors.Errorf("failed to marshal report: %w", err)
 	}
diff --git a/pkg/vex/vex.go b/pkg/vex/vex.go
index 925dbeaa6c..49fd62eccd 100644
--- a/pkg/vex/vex.go
+++ b/pkg/vex/vex.go
@@ -75,7 +75,7 @@ func Filter(ctx context.Context, report *types.Report, opts Options) error {
 	}
 
 	// NOTE: This method call has a side effect on the report
-	bom, err := sbomio.NewEncoder(core.Options{Parents: true}).Encode(*report)
+	bom, err := sbomio.NewEncoder(sbomio.WithParents(), sbomio.ForceRegenerate()).Encode(*report)
 	if err != nil {
 		return xerrors.Errorf("unable to encode the SBOM: %w", err)
 	}
diff --git a/pkg/vex/vex_test.go b/pkg/vex/vex_test.go
index 55c93566e4..3a36154bff 100644
--- a/pkg/vex/vex_test.go
+++ b/pkg/vex/vex_test.go
@@ -665,13 +665,18 @@ func createCycloneDXBOMWithSpringComponent() *core.BOM {
 	bom := core.NewBOM(core.Options{})
 	bom.SerialNumber = "urn:uuid:3e671687-395b-41f5-a30f-a58921a69b79"
 	bom.Version = 1
+	pkgIdentifier := ftypes.PkgIdentifier{
+		// Components got from scanned SBOM files don't have UID
+		BOMRef: springPackage.Identifier.BOMRef,
+		PURL:   springPackage.Identifier.PURL,
+	}
 	// Add the spring component to match vuln1's BOM-Ref
 	springComponent := &core.Component{
 		Type:          core.TypeLibrary,
 		Name:          springPackage.Identifier.PURL.Name,
 		Group:         springPackage.Identifier.PURL.Namespace,
 		Version:       springPackage.Version,
-		PkgIdentifier: springPackage.Identifier,
+		PkgIdentifier: pkgIdentifier,
 	}
 	bom.AddComponent(springComponent)
 	return bom