diff --git a/cmd/sbomgen/scanners.go b/cmd/sbomgen/scanners.go
index be9bf33b3a059..04de0635c09dc 100644
--- a/cmd/sbomgen/scanners.go
+++ b/cmd/sbomgen/scanners.go
@@ -28,7 +28,7 @@ func runScanFS(path string, analyzers []string, fast bool) error {
 	report, err := collector.ScanFilesystem(ctx, path, sbom.ScanOptions{
 		Analyzers: analyzers,
 		Fast:      fast,
-	})
+	}, false)
 	if err != nil {
 		return err
 	}
diff --git a/pkg/sbom/collectors/host/host.go b/pkg/sbom/collectors/host/host.go
index b8a163521ec84..13d75fbcabbc9 100644
--- a/pkg/sbom/collectors/host/host.go
+++ b/pkg/sbom/collectors/host/host.go
@@ -48,7 +48,7 @@ func (c *Collector) Scan(ctx context.Context, request sbom.ScanRequest) sbom.Sca
 	path := request.ID() // for host request, ID == path
 	log.Infof("host scan request [%v]", path)
 
-	report, err := c.trivyCollector.ScanFilesystem(ctx, path, c.opts)
+	report, err := c.trivyCollector.ScanFilesystem(ctx, path, c.opts, true)
 	return sbom.ScanResult{
 		Error:  err,
 		Report: report,
diff --git a/pkg/util/trivy/cache.go b/pkg/util/trivy/cache.go
index 7062457d140cf..27d57cfc3226a 100644
--- a/pkg/util/trivy/cache.go
+++ b/pkg/util/trivy/cache.go
@@ -469,14 +469,16 @@ func (c *persistentCache) collectTelemetry() {
 }
 
 func newMemoryCache() *memoryCache {
-	return &memoryCache{}
+	return &memoryCache{
+		blobs:     make(map[string]types.BlobInfo),
+		artifacts: make(map[string]types.ArtifactInfo),
+	}
 }
 
 type memoryCache struct {
-	blobInfo     *types.BlobInfo
-	blobID       string
-	artifactInfo *types.ArtifactInfo
-	artifactID   string
+	blobs     map[string]types.BlobInfo
+	artifacts map[string]types.ArtifactInfo
+	blobID    string
 }
 
 func (c *memoryCache) MissingBlobs(artifactID string, blobIDs []string) (missingArtifact bool, missingBlobIDs []string, err error) {
@@ -494,45 +496,42 @@ func (c *memoryCache) MissingBlobs(artifactID string, blobIDs []string) (missing
 }
 
 func (c *memoryCache) PutArtifact(artifactID string, artifactInfo types.ArtifactInfo) (err error) {
-	c.artifactInfo = &artifactInfo
-	c.artifactID = artifactID
+	c.artifacts[artifactID] = artifactInfo
 	return nil
 }
 
 func (c *memoryCache) PutBlob(blobID string, blobInfo types.BlobInfo) (err error) {
-	c.blobInfo = &blobInfo
+	c.blobs[blobID] = blobInfo
 	c.blobID = blobID
 	return nil
 }
 
 func (c *memoryCache) DeleteBlobs(blobIDs []string) error {
-	if c.blobInfo != nil {
-		for _, blobID := range blobIDs {
-			if blobID == c.blobID {
-				c.blobInfo = nil
-			}
-		}
+	for _, id := range blobIDs {
+		delete(c.blobs, id)
 	}
 	return nil
 }
 
 func (c *memoryCache) GetArtifact(artifactID string) (artifactInfo types.ArtifactInfo, err error) {
-	if c.artifactInfo != nil && c.artifactID == artifactID {
-		return *c.artifactInfo, nil
+	art, ok := c.artifacts[artifactID]
+	if !ok {
+		return types.ArtifactInfo{}, errors.New("not found")
 	}
-	return types.ArtifactInfo{}, nil
+	return art, nil
 }
 
 func (c *memoryCache) GetBlob(blobID string) (blobInfo types.BlobInfo, err error) {
-	if c.blobInfo != nil && c.blobID == blobID {
-		return *c.blobInfo, nil
+	b, ok := c.blobs[blobID]
+	if !ok {
+		return types.BlobInfo{}, errors.New("not found")
 	}
-	return types.BlobInfo{}, errors.New("not found")
+	return b, nil
 }
 
 func (c *memoryCache) Close() (err error) {
-	c.artifactInfo = nil
-	c.blobInfo = nil
+	c.artifacts = nil
+	c.blobs = nil
 	return nil
 }
 
diff --git a/pkg/util/trivy/containerd.go b/pkg/util/trivy/containerd.go
index 0393e1179bffb..5e4e71f10af80 100644
--- a/pkg/util/trivy/containerd.go
+++ b/pkg/util/trivy/containerd.go
@@ -312,7 +312,7 @@ func (c *Collector) ScanContainerdImageFromFilesystem(ctx context.Context, imgMe
 		}
 	}()
 
-	report, err := c.ScanFilesystem(ctx, imagePath, scanOptions)
+	report, err := c.ScanFilesystem(ctx, imagePath, scanOptions, false)
 	if err != nil {
 		return nil, fmt.Errorf("unable to scan image %s, err: %w", imgMeta.ID, err)
 	}
diff --git a/pkg/util/trivy/trivy.go b/pkg/util/trivy/trivy.go
index f2e7c5d875bea..19f7985ba57c9 100644
--- a/pkg/util/trivy/trivy.go
+++ b/pkg/util/trivy/trivy.go
@@ -285,8 +285,23 @@ func (c *Collector) getCache() (CacheWithCleaner, error) {
 	return c.persistentCache, nil
 }
 
+type fakeArtifact struct {
+	inner     artifact.Artifact
+	forceType artifact.Type
+}
+
+func (fa *fakeArtifact) Inspect(ctx context.Context) (artifact.Reference, error) {
+	ref, err := fa.inner.Inspect(ctx)
+	ref.Type = fa.forceType
+	return ref, err
+}
+
+func (fa *fakeArtifact) Clean(ref artifact.Reference) error {
+	return fa.inner.Clean(ref)
+}
+
 // ScanFilesystem scans the specified directory and logs detailed scan steps.
-func (c *Collector) ScanFilesystem(ctx context.Context, path string, scanOptions sbom.ScanOptions) (sbom.Report, error) {
+func (c *Collector) ScanFilesystem(ctx context.Context, path string, scanOptions sbom.ScanOptions, removeLayer bool) (sbom.Report, error) {
 	// For filesystem scans, it is required to walk the filesystem to get the persistentCache key so caching does not add any value.
 	// TODO: Cache directly the trivy report for container images
 	cache := newMemoryCache()
@@ -296,7 +311,15 @@ func (c *Collector) ScanFilesystem(ctx context.Context, path string, scanOptions
 		return nil, fmt.Errorf("unable to create artifact from fs, err: %w", err)
 	}
 
-	trivyReport, err := c.scan(ctx, fsArtifact, applier.NewApplier(cache))
+	wrapper := &fakeArtifact{
+		inner:     fsArtifact,
+		forceType: artifact.TypeContainerImage,
+	}
+	if removeLayer {
+		wrapper.forceType = artifact.TypeFilesystem
+	}
+
+	trivyReport, err := c.scan(ctx, wrapper, applier.NewApplier(cache))
 	if err != nil {
 		return nil, fmt.Errorf("unable to marshal report to sbom format, err: %w", err)
 	}