diff --git a/keyserver/internal/cross_signing.go b/keyserver/internal/cross_signing.go
index 2281f4bbf..d5e2c2153 100644
--- a/keyserver/internal/cross_signing.go
+++ b/keyserver/internal/cross_signing.go
@@ -362,6 +362,12 @@ func (a *KeyInternalAPI) processSelfSignatures(
 		for targetKeyID, signature := range forTargetUserID {
 			switch sig := signature.CrossSigningBody.(type) {
 			case *gomatrixserverlib.CrossSigningKey:
+				for keyID := range sig.Keys {
+					if gomatrixserverlib.KeyID(strings.SplitN(string(keyID), ":", 1)[1]) == keyID {
+						targetKeyID = keyID // contains the ed25519: or other scheme
+						break
+					}
+				}
 				for originUserID, forOriginUserID := range sig.Signatures {
 					for originKeyID, originSig := range forOriginUserID {
 						if err := a.DB.StoreCrossSigningSigsForTarget(
@@ -373,6 +379,12 @@ func (a *KeyInternalAPI) processSelfSignatures(
 				}
 
 			case *gomatrixserverlib.DeviceKeys:
+				for keyID := range sig.Keys {
+					if gomatrixserverlib.KeyID(strings.SplitN(string(keyID), ":", 1)[1]) == keyID {
+						targetKeyID = keyID // contains the ed25519: or other scheme
+						break
+					}
+				}
 				for originUserID, forOriginUserID := range sig.Signatures {
 					for originKeyID, originSig := range forOriginUserID {
 						if err := a.DB.StoreCrossSigningSigsForTarget(