diff --git a/src/core/init.ts b/src/core/init.ts
index 1c4f14fb..ab3dc55b 100644
--- a/src/core/init.ts
+++ b/src/core/init.ts
@@ -21,6 +21,7 @@ import {
   AI_TOOLS,
   OPENSPEC_DIR_NAME,
   AIToolOption,
+  OPENSPEC_MARKERS,
 } from './config.js';
 import { PALETTE } from './styles/palette.js';
 
@@ -388,7 +389,7 @@ export class InitCommand {
 
     // Validation happens silently in the background
     const extendMode = await this.validate(projectPath, openspecPath);
-    const existingToolStates = await this.getExistingToolStates(projectPath);
+    const existingToolStates = await this.getExistingToolStates(projectPath, extendMode);
 
     this.renderBanner(extendMode);
 
@@ -627,35 +628,78 @@ export class InitCommand {
   }
 
   private async getExistingToolStates(
-    projectPath: string
+    projectPath: string,
+    extendMode: boolean
   ): Promise<Record<string, boolean>> {
-    const states: Record<string, boolean> = {};
-    for (const tool of AI_TOOLS) {
-      states[tool.value] = await this.isToolConfigured(projectPath, tool.value);
+    // Fresh initialization - no tools configured yet
+    if (!extendMode) {
+      return Object.fromEntries(AI_TOOLS.map(t => [t.value, false]));
     }
-    return states;
+
+    // Extend mode - check all tools in parallel for better performance
+    const entries = await Promise.all(
+      AI_TOOLS.map(async (t) => [t.value, await this.isToolConfigured(projectPath, t.value)] as const)
+    );
+    return Object.fromEntries(entries);
   }
 
   private async isToolConfigured(
     projectPath: string,
     toolId: string
   ): Promise<boolean> {
+    // A tool is only considered "configured by OpenSpec" if its files contain OpenSpec markers.
+    // For tools with both config files and slash commands, BOTH must have markers.
+    // For slash commands, at least one file with markers is sufficient (not all required).
+
+    // Helper to check if a file exists and contains OpenSpec markers
+    const fileHasMarkers = async (absolutePath: string): Promise<boolean> => {
+      try {
+        const content = await FileSystemUtils.readFile(absolutePath);
+        return content.includes(OPENSPEC_MARKERS.start) && content.includes(OPENSPEC_MARKERS.end);
+      } catch {
+        return false;
+      }
+    };
+
+    let hasConfigFile = false;
+    let hasSlashCommands = false;
+
+    // Check if the tool has a config file with OpenSpec markers
     const configFile = ToolRegistry.get(toolId)?.configFileName;
-    if (
-      configFile &&
-      (await FileSystemUtils.fileExists(path.join(projectPath, configFile)))
-    )
-      return true;
+    if (configFile) {
+      const configPath = path.join(projectPath, configFile);
+      hasConfigFile = (await FileSystemUtils.fileExists(configPath)) && (await fileHasMarkers(configPath));
+    }
 
+    // Check if any slash command file exists with OpenSpec markers
     const slashConfigurator = SlashCommandRegistry.get(toolId);
-    if (!slashConfigurator) return false;
-    for (const target of slashConfigurator.getTargets()) {
-      const absolute = slashConfigurator.resolveAbsolutePath(
-        projectPath,
-        target.id
-      );
-      if (await FileSystemUtils.fileExists(absolute)) return true;
+    if (slashConfigurator) {
+      for (const target of slashConfigurator.getTargets()) {
+        const absolute = slashConfigurator.resolveAbsolutePath(projectPath, target.id);
+        if ((await FileSystemUtils.fileExists(absolute)) && (await fileHasMarkers(absolute))) {
+          hasSlashCommands = true;
+          break; // At least one file with markers is sufficient
+        }
+      }
+    }
+
+    // Tool is only configured if BOTH exist with markers
+    // OR if the tool has no config file requirement (slash commands only)
+    // OR if the tool has no slash commands requirement (config file only)
+    const hasConfigFileRequirement = configFile !== undefined;
+    const hasSlashCommandRequirement = slashConfigurator !== undefined;
+
+    if (hasConfigFileRequirement && hasSlashCommandRequirement) {
+      // Both are required - both must be present with markers
+      return hasConfigFile && hasSlashCommands;
+    } else if (hasConfigFileRequirement) {
+      // Only config file required
+      return hasConfigFile;
+    } else if (hasSlashCommandRequirement) {
+      // Only slash commands required
+      return hasSlashCommands;
     }
+
     return false;
   }
 
diff --git a/test/core/init.test.ts b/test/core/init.test.ts
index 99be9740..4c7a91d4 100644
--- a/test/core/init.test.ts
+++ b/test/core/init.test.ts
@@ -1051,6 +1051,87 @@ describe('InitCommand', () => {
     });
   });
 
+  describe('already configured detection', () => {
+    it('should NOT show tools as already configured in fresh project with existing CLAUDE.md', async () => {
+      // Simulate user having their own CLAUDE.md before running openspec init
+      const claudePath = path.join(testDir, 'CLAUDE.md');
+      await fs.writeFile(claudePath, '# My Custom Claude Instructions\n');
+
+      queueSelections('claude', DONE);
+
+      await initCommand.execute(testDir);
+
+      // In the first run (non-interactive mode via queueSelections),
+      // the prompt is called with configured: false for claude
+      const firstCallArgs = mockPrompt.mock.calls[0][0];
+      const claudeChoice = firstCallArgs.choices.find(
+        (choice: any) => choice.value === 'claude'
+      );
+
+      expect(claudeChoice.configured).toBe(false);
+    });
+
+    it('should NOT show tools as already configured in fresh project with existing slash commands', async () => {
+      // Simulate user having their own custom slash commands
+      const customCommandDir = path.join(testDir, '.claude/commands/custom');
+      await fs.mkdir(customCommandDir, { recursive: true });
+      await fs.writeFile(
+        path.join(customCommandDir, 'mycommand.md'),
+        '# My Custom Command\n'
+      );
+
+      queueSelections('claude', DONE);
+
+      await initCommand.execute(testDir);
+
+      const firstCallArgs = mockPrompt.mock.calls[0][0];
+      const claudeChoice = firstCallArgs.choices.find(
+        (choice: any) => choice.value === 'claude'
+      );
+
+      expect(claudeChoice.configured).toBe(false);
+    });
+
+    it('should show tools as already configured in extend mode', async () => {
+      // First initialization
+      queueSelections('claude', DONE);
+      await initCommand.execute(testDir);
+
+      // Second initialization (extend mode)
+      queueSelections('cursor', DONE);
+      await initCommand.execute(testDir);
+
+      const secondCallArgs = mockPrompt.mock.calls[1][0];
+      const claudeChoice = secondCallArgs.choices.find(
+        (choice: any) => choice.value === 'claude'
+      );
+
+      expect(claudeChoice.configured).toBe(true);
+    });
+
+    it('should NOT show already configured for Codex in fresh init even with global prompts', async () => {
+      // Create global Codex prompts (simulating previous installation)
+      const codexPromptsDir = path.join(testDir, '.codex/prompts');
+      await fs.mkdir(codexPromptsDir, { recursive: true });
+      await fs.writeFile(
+        path.join(codexPromptsDir, 'openspec-proposal.md'),
+        '# Existing prompt\n'
+      );
+
+      queueSelections('claude', DONE);
+
+      await initCommand.execute(testDir);
+
+      const firstCallArgs = mockPrompt.mock.calls[0][0];
+      const codexChoice = firstCallArgs.choices.find(
+        (choice: any) => choice.value === 'codex'
+      );
+
+      // In fresh init, even global tools should not show as configured
+      expect(codexChoice.configured).toBe(false);
+    });
+  });
+
   describe('error handling', () => {
     it('should provide helpful error for insufficient permissions', async () => {
       // This is tricky to test cross-platform, but we can test the error message