diff --git a/pkg/sbom/io/decode.go b/pkg/sbom/io/decode.go
index 917684962d20..4f5ac4cd19bb 100644
--- a/pkg/sbom/io/decode.go
+++ b/pkg/sbom/io/decode.go
@@ -10,6 +10,7 @@ import (
 	debver "github.com/knqyf263/go-deb-version"
 	rpmver "github.com/knqyf263/go-rpm-version"
 	"github.com/package-url/packageurl-go"
+	"github.com/samber/lo"
 	"golang.org/x/exp/maps"
 	"golang.org/x/xerrors"
 
@@ -375,8 +376,12 @@ func (m *Decoder) addOrphanPkgs(sbom *types.SBOM) error {
 
 		// TODO: mismatch between the OS and the packages should be rejected.
 		// e.g. OS: debian, Packages: rpm
-		sort.Sort(pkgs)
-		sbom.Packages = append(sbom.Packages, ftypes.PackageInfo{Packages: pkgs})
+
+		// `applier` package merges `PackageInfo` elements  along the filepath,
+		// but sbom files may not contain filepath for OS packages.
+		// In these cases we will overwrite `PackageInfo` and miss some `Packages`.
+		// This is why we need to merge all found `Packages` into one `PackageInfo`.
+		sbom.Packages = appendOrphanPkgsToPackageInfo(sbom.Packages, pkgs)
 
 		break // Just take the first element
 	}
@@ -391,3 +396,25 @@ func (m *Decoder) addOrphanPkgs(sbom *types.SBOM) error {
 	}
 	return nil
 }
+
+// appendOrphanPkgsToPackageInfo merges `orphanPkgs` into `packages[0]` (the comparison is done by PURL).
+// Merged `Packages` are sorted.
+func appendOrphanPkgsToPackageInfo(packages []ftypes.PackageInfo, orphanPkgs ftypes.Packages) []ftypes.PackageInfo {
+	// Length of `packages` can be only 0 or 1
+	// packages[].FilePath is always empty
+	// cf. https://github.com/aquasecurity/trivy/blob/09e50ce6a82073ba62f1732d5aa0cd2701578693/pkg/sbom/io/decode.go#L331
+	var pkgs ftypes.Packages
+	if len(packages) == 1 { //
+		pkgs = packages[0].Packages
+	}
+	pkgs = append(pkgs, orphanPkgs...)
+	pkgs = lo.UniqBy(pkgs, func(pkg ftypes.Package) string {
+		return pkg.Identifier.PURL.String()
+	})
+	sort.Sort(pkgs)
+	return []ftypes.PackageInfo{
+		{
+			Packages: pkgs,
+		},
+	}
+}