diff --git a/README.md b/README.md
index 20ddbd6..600371a 100644
--- a/README.md
+++ b/README.md
@@ -44,6 +44,11 @@ lnk init
 
 This creates `$XDG_CONFIG_HOME/lnk` (or `~/.config/lnk`) and initializes a Git repository with `main` as the default branch.
 
+**Safety Features:**
+- **Idempotent**: Running `lnk init` multiple times is safe and won't break existing repositories
+- **Repository Protection**: Won't overwrite existing non-lnk Git repositories (exits with error)
+- **Fresh Repository Detection**: Automatically detects if a directory contains an existing repository
+
 ### Initialize with remote
 
 ```bash
@@ -54,6 +59,11 @@ lnk init -r git@github.com:user/dotfiles.git
 
 This initializes the repository with `main` as the default branch and adds the specified URL as the `origin` remote, allowing you to sync your dotfiles with a Git hosting service.
 
+**Remote Handling:**
+- **Idempotent**: Adding the same remote URL multiple times is safe (no-op)
+- **Conflict Detection**: Adding different remote URLs fails with clear error message
+- **Existing Remote Support**: Works safely with repositories that already have remotes configured
+
 ### Add a file
 
 ```bash
@@ -87,6 +97,12 @@ lnk init
 # Initialize with remote for syncing with GitHub
 lnk init --remote https://github.com/user/dotfiles.git
 
+# Running init again is safe (idempotent)
+lnk init  # No error, no changes
+
+# Adding same remote again is safe
+lnk init -r https://github.com/user/dotfiles.git  # No error, no changes
+
 # Add some dotfiles
 lnk add ~/.bashrc
 lnk add ~/.vimrc
@@ -103,11 +119,27 @@ git log --oneline
 git push origin main
 ```
 
+### Safety Examples
+
+```bash
+# Attempting to init over existing non-lnk repository
+mkdir ~/.config/lnk && cd ~/.config/lnk
+git init && echo "important" > file.txt && git add . && git commit -m "important data"
+cd ~
+lnk init  # ERROR: Won't overwrite existing repository
+
+# Attempting to add conflicting remote
+lnk init -r https://github.com/user/repo1.git
+lnk init -r https://github.com/user/repo2.git  # ERROR: Different URL conflict
+```
+
 ## Error Handling
 
 - Adding a nonexistent file: exits with error
 - Adding a directory: exits with "directories are not supported"
 - Removing a non-symlink: exits with "file is not managed by lnk"
+- **Repository conflicts**: `lnk init` protects existing non-lnk repositories from accidental overwrite
+- **Remote conflicts**: Adding different remote URLs to existing remotes fails with descriptive error
 - Git operations show stderr output on failure
 
 ## Development
diff --git a/internal/core/lnk.go b/internal/core/lnk.go
index 797a9d1..72e9442 100644
--- a/internal/core/lnk.go
+++ b/internal/core/lnk.go
@@ -48,7 +48,19 @@ func (l *Lnk) Init() error {
 		return fmt.Errorf("failed to create lnk directory: %w", err)
 	}
 
-	// Initialize Git repository
+	// Check if there's already a Git repository
+	if l.git.IsGitRepository() {
+		// Repository exists, check if it's a lnk repository
+		if l.git.IsLnkRepository() {
+			// It's a lnk repository, init is idempotent - do nothing
+			return nil
+		} else {
+			// It's not a lnk repository, error to prevent data loss
+			return fmt.Errorf("directory %s appears to contain an existing Git repository that is not managed by lnk. Please backup or move the existing repository before initializing lnk", l.repoPath)
+		}
+	}
+
+	// No existing repository, initialize Git repository
 	if err := l.git.Init(); err != nil {
 		return fmt.Errorf("failed to initialize git repository: %w", err)
 	}
diff --git a/internal/git/git.go b/internal/git/git.go
index b87d3dc..2220a35 100644
--- a/internal/git/git.go
+++ b/internal/git/git.go
@@ -26,13 +26,13 @@ func (g *Git) Init() error {
 	cmd := exec.Command("git", "init", "-b", "main")
 	cmd.Dir = g.repoPath
 
-	output, err := cmd.CombinedOutput()
+	_, err := cmd.CombinedOutput()
 	if err != nil {
 		// Fallback to regular init + branch rename for older Git versions
 		cmd = exec.Command("git", "init")
 		cmd.Dir = g.repoPath
 
-		output, err = cmd.CombinedOutput()
+		output, err := cmd.CombinedOutput()
 		if err != nil {
 			return fmt.Errorf("git init failed: %w\nOutput: %s", err, string(output))
 		}
@@ -51,6 +51,19 @@ func (g *Git) Init() error {
 
 // AddRemote adds a remote to the repository
 func (g *Git) AddRemote(name, url string) error {
+	// Check if remote already exists
+	existingURL, err := g.getRemoteURL(name)
+	if err == nil {
+		// Remote exists, check if URL matches
+		if existingURL == url {
+			// Same URL, idempotent - do nothing
+			return nil
+		}
+		// Different URL, error
+		return fmt.Errorf("remote %s already exists with different URL: %s (trying to add: %s)", name, existingURL, url)
+	}
+
+	// Remote doesn't exist, add it
 	cmd := exec.Command("git", "remote", "add", name, url)
 	cmd.Dir = g.repoPath
 
@@ -62,6 +75,58 @@ func (g *Git) AddRemote(name, url string) error {
 	return nil
 }
 
+// getRemoteURL returns the URL for a remote, or error if not found
+func (g *Git) getRemoteURL(name string) (string, error) {
+	cmd := exec.Command("git", "remote", "get-url", name)
+	cmd.Dir = g.repoPath
+
+	output, err := cmd.Output()
+	if err != nil {
+		return "", err
+	}
+
+	return strings.TrimSpace(string(output)), nil
+}
+
+// IsGitRepository checks if the directory contains a Git repository
+func (g *Git) IsGitRepository() bool {
+	gitDir := filepath.Join(g.repoPath, ".git")
+	_, err := os.Stat(gitDir)
+	return err == nil
+}
+
+// IsLnkRepository checks if the repository appears to be managed by lnk
+func (g *Git) IsLnkRepository() bool {
+	if !g.IsGitRepository() {
+		return false
+	}
+
+	// Check if this looks like a lnk repository
+	// We consider it a lnk repo if:
+	// 1. It has no commits (fresh repo), OR
+	// 2. All commits start with "lnk:" pattern
+
+	commits, err := g.GetCommits()
+	if err != nil {
+		return false
+	}
+
+	// If no commits, it's a fresh repo - could be lnk
+	if len(commits) == 0 {
+		return true
+	}
+
+	// If all commits start with "lnk:", it's definitely ours
+	// If ANY commit doesn't start with "lnk:", it's probably not ours
+	for _, commit := range commits {
+		if !strings.HasPrefix(commit, "lnk:") {
+			return false
+		}
+	}
+
+	return true
+}
+
 // AddAndCommit stages a file and commits it
 func (g *Git) AddAndCommit(filename, message string) error {
 	// Stage the file
@@ -176,10 +241,11 @@ func (g *Git) GetCommits() ([]string, error) {
 	cmd := exec.Command("git", "log", "--oneline", "--format=%s")
 	cmd.Dir = g.repoPath
 
-	output, err := cmd.Output()
+	output, err := cmd.CombinedOutput()
 	if err != nil {
 		// If there are no commits yet, return empty slice
-		if strings.Contains(string(output), "does not have any commits yet") {
+		outputStr := string(output)
+		if strings.Contains(outputStr, "does not have any commits yet") {
 			return []string{}, nil
 		}
 		return nil, fmt.Errorf("git log failed: %w", err)
diff --git a/test/integration_test.go b/test/integration_test.go
index 9e02bea..e15445a 100644
--- a/test/integration_test.go
+++ b/test/integration_test.go
@@ -230,6 +230,116 @@ func (suite *LnkIntegrationTestSuite) TestInitWithRemote() {
 	suite.Equal(remoteURL, strings.TrimSpace(string(output)))
 }
 
+func (suite *LnkIntegrationTestSuite) TestInitIdempotent() {
+	// Test that running init multiple times is safe
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+
+	// Add a file to the repo to ensure it's not lost
+	testFile := filepath.Join(lnkDir, "test.txt")
+	err = os.WriteFile(testFile, []byte("test content"), 0644)
+	suite.Require().NoError(err)
+
+	// Run init again - should be idempotent
+	err = suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// File should still exist
+	suite.FileExists(testFile)
+	content, err := os.ReadFile(testFile)
+	suite.Require().NoError(err)
+	suite.Equal("test content", string(content))
+}
+
+func (suite *LnkIntegrationTestSuite) TestInitWithExistingRemote() {
+	// Test init with remote when remote already exists (same URL)
+	remoteURL := "https://github.com/user/dotfiles.git"
+
+	// First init with remote
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+	err = suite.lnk.AddRemote("origin", remoteURL)
+	suite.Require().NoError(err)
+
+	// Init again with same remote should be idempotent
+	err = suite.lnk.Init()
+	suite.Require().NoError(err)
+	err = suite.lnk.AddRemote("origin", remoteURL)
+	suite.Require().NoError(err)
+
+	// Verify remote is still correct
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	cmd := exec.Command("git", "remote", "get-url", "origin")
+	cmd.Dir = lnkDir
+	output, err := cmd.Output()
+	suite.Require().NoError(err)
+	suite.Equal(remoteURL, strings.TrimSpace(string(output)))
+}
+
+func (suite *LnkIntegrationTestSuite) TestInitWithDifferentRemote() {
+	// Test init with different remote when remote already exists
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Add first remote
+	err = suite.lnk.AddRemote("origin", "https://github.com/user/dotfiles.git")
+	suite.Require().NoError(err)
+
+	// Try to add different remote - should error
+	err = suite.lnk.AddRemote("origin", "https://github.com/user/other-repo.git")
+	suite.Error(err)
+	suite.Contains(err.Error(), "already exists with different URL")
+}
+
+func (suite *LnkIntegrationTestSuite) TestInitWithNonLnkRepo() {
+	// Test init when directory contains a non-lnk Git repository
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	err := os.MkdirAll(lnkDir, 0755)
+	suite.Require().NoError(err)
+
+	// Create a non-lnk git repo in the lnk directory
+	cmd := exec.Command("git", "init")
+	cmd.Dir = lnkDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Add some content to make it look like a real repo
+	testFile := filepath.Join(lnkDir, "important-file.txt")
+	err = os.WriteFile(testFile, []byte("important data"), 0644)
+	suite.Require().NoError(err)
+
+	// Configure git and commit
+	cmd = exec.Command("git", "config", "user.name", "Test User")
+	cmd.Dir = lnkDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "config", "user.email", "test@example.com")
+	cmd.Dir = lnkDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "add", "important-file.txt")
+	cmd.Dir = lnkDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "commit", "-m", "important commit")
+	cmd.Dir = lnkDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Now try to init lnk - should error to protect existing repo
+	err = suite.lnk.Init()
+	suite.Error(err)
+	suite.Contains(err.Error(), "appears to contain an existing Git repository")
+
+	// Verify the original file is still there
+	suite.FileExists(testFile)
+}
+
 func TestLnkIntegrationSuite(t *testing.T) {
 	suite.Run(t, new(LnkIntegrationTestSuite))
 }