diff --git a/cmd/bd/doctor/claude.go b/cmd/bd/doctor/claude.go
index 02bc1eb3..5327162a 100644
--- a/cmd/bd/doctor/claude.go
+++ b/cmd/bd/doctor/claude.go
@@ -433,20 +433,46 @@ func GetClaudePluginVersion() (version string, installed bool, err error) {
 		return "", false, fmt.Errorf("unable to read plugin file: %w", err)
 	}
 
-	// Parse JSON - handle nested structure
-	var pluginData struct {
+	// First, determine the format version
+	var versionCheck struct {
 		Version int `json:"version"`
+	}
+	if err := json.Unmarshal(data, &versionCheck); err != nil {
+		return "", false, fmt.Errorf("unable to parse plugin file: %w", err)
+	}
+
+	// Handle version 2 format (GH#741): plugins map contains arrays
+	if versionCheck.Version == 2 {
+		var pluginDataV2 struct {
+			Plugins map[string][]struct {
+				Version string `json:"version"`
+				Scope   string `json:"scope"`
+			} `json:"plugins"`
+		}
+		if err := json.Unmarshal(data, &pluginDataV2); err != nil {
+			return "", false, fmt.Errorf("unable to parse plugin file v2: %w", err)
+		}
+
+		// Look for beads plugin - take first entry from the array
+		if entries, ok := pluginDataV2.Plugins["beads@beads-marketplace"]; ok && len(entries) > 0 {
+			return entries[0].Version, true, nil
+		}
+		return "", false, nil
+	}
+
+	// Handle version 1 format (original): plugins map contains structs directly
+	var pluginDataV1 struct {
 		Plugins map[string]struct {
 			Version string `json:"version"`
 		} `json:"plugins"`
 	}
 
-	if err := json.Unmarshal(data, &pluginData); err != nil {
+	if err := json.Unmarshal(data, &pluginDataV1); err != nil {
 		return "", false, fmt.Errorf("unable to parse plugin file: %w", err)
 	}
 
 	// Look for beads plugin
-	if plugin, ok := pluginData.Plugins["beads@beads-marketplace"]; ok {
+	if plugin, ok := pluginDataV1.Plugins["beads@beads-marketplace"]; ok {
 		return plugin.Version, true, nil
 	}
 
diff --git a/cmd/bd/doctor_test.go b/cmd/bd/doctor_test.go
index fb485036..0da151a8 100644
--- a/cmd/bd/doctor_test.go
+++ b/cmd/bd/doctor_test.go
@@ -804,7 +804,7 @@ func TestGetClaudePluginVersion(t *testing.T) {
 		expectError     bool
 	}{
 		{
-			name: "plugin installed",
+			name: "plugin installed v1 format",
 			pluginJSON: `{
 				"version": 1,
 				"plugins": {
@@ -818,7 +818,46 @@ func TestGetClaudePluginVersion(t *testing.T) {
 			expectError:     false,
 		},
 		{
-			name: "plugin not installed",
+			name: "plugin installed v2 format (GH#741)",
+			pluginJSON: `{
+				"version": 2,
+				"plugins": {
+					"beads@beads-marketplace": [
+						{
+							"scope": "user",
+							"installPath": "/path/to/plugin",
+							"version": "1.0.0",
+							"installedAt": "2025-11-25T19:20:27.889Z",
+							"lastUpdated": "2025-11-25T19:20:27.889Z",
+							"gitCommitSha": "abc123",
+							"isLocal": true
+						}
+					]
+				}
+			}`,
+			expectInstalled: true,
+			expectVersion:   "1.0.0",
+			expectError:     false,
+		},
+		{
+			name: "plugin not installed v2 format",
+			pluginJSON: `{
+				"version": 2,
+				"plugins": {
+					"other-plugin@marketplace": [
+						{
+							"scope": "user",
+							"version": "2.0.0"
+						}
+					]
+				}
+			}`,
+			expectInstalled: false,
+			expectVersion:   "",
+			expectError:     false,
+		},
+		{
+			name: "plugin not installed v1 format",
 			pluginJSON: `{
 				"version": 1,
 				"plugins": {