diff --git a/changelog/fragments/bundle-scorecard-input-dir.yaml b/changelog/fragments/bundle-scorecard-input-dir.yaml
new file mode 100644
index 00000000000..615eab88b24
--- /dev/null
+++ b/changelog/fragments/bundle-scorecard-input-dir.yaml
@@ -0,0 +1,9 @@
+entries:
+  - description: >
+      Fixed `generate bundle` so that bundle metadata (`bundle.Dockerfile` and
+      `annotations.yaml`) references the scorecard config when the manifests are read
+      with `--input-dir`. Previously the config was written to the output directory
+      but looked up in the input directory, so the scorecard labels and `COPY` line
+      were omitted.
+    kind: bugfix
+    breaking: false
diff --git a/internal/cmd/operator-sdk/generate/bundle/bundle.go b/internal/cmd/operator-sdk/generate/bundle/bundle.go
index 36e2ca54760..8ac771891f3 100644
--- a/internal/cmd/operator-sdk/generate/bundle/bundle.go
+++ b/internal/cmd/operator-sdk/generate/bundle/bundle.go
@@ -291,20 +291,34 @@ func (c bundleCmd) runMetadata() error {
 		}
 	}
 
-	scorecardConfigPath := filepath.Join(bundleRoot, scorecard.DefaultConfigDir, scorecard.ConfigFileName)
-
 	bundleMetadata := bundleutil.BundleMetaData{
 		BundleDir:            c.outputDir,
 		PackageName:          c.packageName,
 		Channels:             c.channels,
 		DefaultChannel:       c.defaultChannel,
 		OtherLabels:          metricsannotations.MakeBundleMetadataLabels(c.layout),
-		IsScoreConfigPresent: genutil.IsExist(scorecardConfigPath),
+		IsScoreConfigPresent: hasScorecardConfig(bundleRoot, c.outputDir),
 	}
 
 	return bundleMetadata.GenerateMetadata()
 }
 
+// hasScorecardConfig reports whether a scorecard config exists in any of the given
+// bundle directories. The config is written to the output directory by runManifests,
+// which differs from the input directory when manifests are read from --input-dir,
+// so both must be checked.
+func hasScorecardConfig(dirs ...string) bool {
+	for _, dir := range dirs {
+		if dir == "" {
+			continue
+		}
+		if genutil.IsExist(filepath.Join(dir, scorecard.DefaultConfigDir, scorecard.ConfigFileName)) {
+			return true
+		}
+	}
+	return false
+}
+
 // pinImages is used to replace all image tags in the given manifests with digests
 func (c bundleCmd) pinImages(manifestPath string) error {
 	manifests, err := pullspec.FromDirectory(manifestPath, nil)
diff --git a/internal/cmd/operator-sdk/generate/bundle/bundle_test.go b/internal/cmd/operator-sdk/generate/bundle/bundle_test.go
new file mode 100644
index 00000000000..b404696147c
--- /dev/null
+++ b/internal/cmd/operator-sdk/generate/bundle/bundle_test.go
@@ -0,0 +1,48 @@
+// Copyright 2026 The Operator-SDK Authors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package bundle
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/operator-framework/operator-sdk/internal/scorecard"
+)
+
+func TestHasScorecardConfig(t *testing.T) {
+	inputDir := t.TempDir()
+	outputDir := t.TempDir()
+
+	if hasScorecardConfig(inputDir, outputDir) {
+		t.Fatal("expected no scorecard config in empty directories")
+	}
+
+	// The config is written to the output directory when manifests come from --input-dir.
+	cfgDir := filepath.Join(outputDir, filepath.FromSlash(scorecard.DefaultConfigDir))
+	if err := os.MkdirAll(cfgDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(cfgDir, scorecard.ConfigFileName), []byte("kind: Configuration\n"), 0666); err != nil {
+		t.Fatal(err)
+	}
+
+	if !hasScorecardConfig(inputDir, outputDir) {
+		t.Fatal("expected scorecard config to be found in the output directory")
+	}
+	if hasScorecardConfig(inputDir, "") {
+		t.Fatal("expected no scorecard config when only the empty input directory is checked")
+	}
+}