diff --git a/apps/macos/Sources/Clawdis/AgentWorkspace.swift b/apps/macos/Sources/Clawdis/AgentWorkspace.swift
index 1aaaa4d43..565666da1 100644
--- a/apps/macos/Sources/Clawdis/AgentWorkspace.swift
+++ b/apps/macos/Sources/Clawdis/AgentWorkspace.swift
@@ -11,6 +11,10 @@ enum AgentWorkspace {
     private static let templateDirname = "templates"
     static let identityStartMarker = "<!-- clawdis:identity:start -->"
     static let identityEndMarker = "<!-- clawdis:identity:end -->"
+    enum BootstrapSafety: Equatable {
+        case safe
+        case unsafe(reason: String)
+    }
 
     static func displayPath(for url: URL) -> String {
         let home = FileManager.default.homeDirectoryForCurrentUser.path
@@ -33,6 +37,31 @@ enum AgentWorkspace {
         workspaceURL.appendingPathComponent(self.agentsFilename)
     }
 
+    static func bootstrapSafety(for workspaceURL: URL) -> BootstrapSafety {
+        let fm = FileManager.default
+        var isDir: ObjCBool = false
+        if !fm.fileExists(atPath: workspaceURL.path, isDirectory: &isDir) {
+            return .safe
+        }
+        if !isDir.boolValue {
+            return .unsafe(reason: "Workspace path points to a file.")
+        }
+        let agentsURL = self.agentsURL(workspaceURL: workspaceURL)
+        if fm.fileExists(atPath: agentsURL.path) {
+            return .safe
+        }
+        do {
+            let contents = try fm.contentsOfDirectory(atPath: workspaceURL.path)
+            let ignored: Set<String> = [".DS_Store", ".git", ".gitignore"]
+            let filtered = contents.filter { !ignored.contains($0) }
+            return filtered.isEmpty
+                ? .safe
+                : .unsafe(reason: "Folder isn't empty. Choose a new folder or add AGENTS.md first.")
+        } catch {
+            return .unsafe(reason: "Couldn't inspect the workspace folder.")
+        }
+    }
+
     static func bootstrap(workspaceURL: URL) throws -> URL {
         try FileManager.default.createDirectory(at: workspaceURL, withIntermediateDirectories: true)
         let agentsURL = self.agentsURL(workspaceURL: workspaceURL)
diff --git a/apps/macos/Sources/Clawdis/Onboarding.swift b/apps/macos/Sources/Clawdis/Onboarding.swift
index 3db1daeda..293027dc5 100644
--- a/apps/macos/Sources/Clawdis/Onboarding.swift
+++ b/apps/macos/Sources/Clawdis/Onboarding.swift
@@ -1378,13 +1378,18 @@ struct OnboardingView: View {
         guard self.state.connectionMode == .local else { return }
         let configured = ClawdisConfigFile.inboundWorkspace()
         let url = AgentWorkspace.resolveWorkspaceURL(from: configured)
-        do {
-            _ = try AgentWorkspace.bootstrap(workspaceURL: url)
-            if (configured ?? "").trimmingCharacters(in: .whitespacesAndNewlines).isEmpty {
-                ClawdisConfigFile.setInboundWorkspace(AgentWorkspace.displayPath(for: url))
+        switch AgentWorkspace.bootstrapSafety(for: url) {
+        case .safe:
+            do {
+                _ = try AgentWorkspace.bootstrap(workspaceURL: url)
+                if (configured ?? "").trimmingCharacters(in: .whitespacesAndNewlines).isEmpty {
+                    ClawdisConfigFile.setInboundWorkspace(AgentWorkspace.displayPath(for: url))
+                }
+            } catch {
+                self.workspaceStatus = "Failed to create workspace: \(error.localizedDescription)"
             }
-        } catch {
-            self.workspaceStatus = "Failed to create workspace: \(error.localizedDescription)"
+        case let .unsafe(reason):
+            self.workspaceStatus = "Workspace not touched: \(reason)"
         }
     }
 
@@ -1426,6 +1431,10 @@ struct OnboardingView: View {
 
         do {
             let url = AgentWorkspace.resolveWorkspaceURL(from: self.workspacePath)
+            if case let .unsafe(reason) = AgentWorkspace.bootstrapSafety(for: url) {
+                self.workspaceStatus = "Workspace not created: \(reason)"
+                return
+            }
             _ = try AgentWorkspace.bootstrap(workspaceURL: url)
             self.workspacePath = AgentWorkspace.displayPath(for: url)
             self.workspaceStatus = "Workspace ready at \(self.workspacePath)"
diff --git a/apps/macos/Tests/ClawdisIPCTests/AgentWorkspaceTests.swift b/apps/macos/Tests/ClawdisIPCTests/AgentWorkspaceTests.swift
index 7a6ef8429..507f601b7 100644
--- a/apps/macos/Tests/ClawdisIPCTests/AgentWorkspaceTests.swift
+++ b/apps/macos/Tests/ClawdisIPCTests/AgentWorkspaceTests.swift
@@ -48,4 +48,40 @@ struct AgentWorkspaceTests {
         let second = try AgentWorkspace.bootstrap(workspaceURL: tmp)
         #expect(second == agentsURL)
     }
+
+    @Test
+    func bootstrapSafetyRejectsNonEmptyFolderWithoutAgents() throws {
+        let tmp = FileManager.default.temporaryDirectory
+            .appendingPathComponent("clawdis-ws-\(UUID().uuidString)", isDirectory: true)
+        defer { try? FileManager.default.removeItem(at: tmp) }
+        try FileManager.default.createDirectory(at: tmp, withIntermediateDirectories: true)
+        let marker = tmp.appendingPathComponent("notes.txt")
+        try "hello".write(to: marker, atomically: true, encoding: .utf8)
+
+        let result = AgentWorkspace.bootstrapSafety(for: tmp)
+        switch result {
+        case .unsafe:
+            break
+        case .safe:
+            #expect(false, "Expected unsafe bootstrap safety result.")
+        }
+    }
+
+    @Test
+    func bootstrapSafetyAllowsExistingAgentsFile() throws {
+        let tmp = FileManager.default.temporaryDirectory
+            .appendingPathComponent("clawdis-ws-\(UUID().uuidString)", isDirectory: true)
+        defer { try? FileManager.default.removeItem(at: tmp) }
+        try FileManager.default.createDirectory(at: tmp, withIntermediateDirectories: true)
+        let agents = tmp.appendingPathComponent(AgentWorkspace.agentsFilename)
+        try "# AGENTS.md".write(to: agents, atomically: true, encoding: .utf8)
+
+        let result = AgentWorkspace.bootstrapSafety(for: tmp)
+        switch result {
+        case .safe:
+            break
+        case .unsafe:
+            #expect(false, "Expected safe bootstrap safety result.")
+        }
+    }
 }
diff --git a/docs/onboarding.md b/docs/onboarding.md
index ef1c7da17..ab82062ba 100644
--- a/docs/onboarding.md
+++ b/docs/onboarding.md
@@ -94,7 +94,8 @@ Once setup is complete, the user can switch to the normal chat (`main`) via the
 
 We no longer collect identity in the onboarding wizard. Instead, the **first agent run** performs a playful bootstrap ritual using files in the workspace:
 
-- Workspace is created implicitly (default `~/.clawdis/workspace`) when local is selected.
+- Workspace is created implicitly (default `~/.clawdis/workspace`) when local is selected,
+  but only if the folder is empty or already contains `AGENTS.md`.
 - Files are seeded: `AGENTS.md`, `BOOTSTRAP.md`, `IDENTITY.md`, `USER.md`.
 - `BOOTSTRAP.md` tells the agent to keep it conversational:
   - open with a cute hello