diff --git a/cmd/bd/init.go b/cmd/bd/init.go
index 68ad3c8b..b89bacd7 100644
--- a/cmd/bd/init.go
+++ b/cmd/bd/init.go
@@ -287,16 +287,13 @@ With --stealth: configures per-repository git settings for invisible beads usage
 			os.Exit(1)
 		}
 
-		// Set sync.branch: use explicit --branch flag, or auto-detect current branch
-		// This ensures bd sync --status works after bd init
-		if branch == "" && isGitRepo() {
-			// Auto-detect current branch if not specified
-			currentBranch, err := getGitBranch()
-			if err == nil && currentBranch != "" {
-				branch = currentBranch
-			}
-		}
-
+		// Set sync.branch only if explicitly specified via --branch flag
+		// GH#807: Do NOT auto-detect current branch - if sync.branch is set to main/master,
+		// the worktree created by bd sync will check out main, preventing the user from
+		// checking out main in their working directory (git error: "'main' is already checked out")
+		//
+		// When --branch is not specified, bd sync will commit directly to the current branch
+		// (the original behavior before sync branch feature)
 		if branch != "" {
 			if err := syncbranch.Set(ctx, store, branch); err != nil {
 				fmt.Fprintf(os.Stderr, "Error: failed to set sync branch: %v\n", err)
diff --git a/internal/syncbranch/syncbranch.go b/internal/syncbranch/syncbranch.go
index c5b6e4e7..c1577305 100644
--- a/internal/syncbranch/syncbranch.go
+++ b/internal/syncbranch/syncbranch.go
@@ -65,6 +65,23 @@ func ValidateBranchName(name string) error {
 	return nil
 }
 
+// ValidateSyncBranchName checks if a branch name is valid for use as sync.branch.
+// GH#807: Setting sync.branch to 'main' or 'master' causes problems because the
+// worktree mechanism will check out that branch, preventing the user from checking
+// it out in their working directory.
+func ValidateSyncBranchName(name string) error {
+	if err := ValidateBranchName(name); err != nil {
+		return err
+	}
+
+	// GH#807: Reject main/master as sync branch - these cause worktree conflicts
+	if name == "main" || name == "master" {
+		return fmt.Errorf("cannot use '%s' as sync branch: git worktrees prevent checking out the same branch in multiple locations. Use a dedicated branch like 'beads-sync' instead", name)
+	}
+
+	return nil
+}
+
 // Get retrieves the sync branch configuration with the following precedence:
 // 1. BEADS_SYNC_BRANCH environment variable
 // 2. sync-branch from config.yaml (version controlled, shared across clones)
@@ -178,7 +195,8 @@ func getConfigFromDB(dbPath string, key string) string {
 
 // Set stores the sync branch configuration in the database
 func Set(ctx context.Context, store storage.Storage, branch string) error {
-	if err := ValidateBranchName(branch); err != nil {
+	// GH#807: Use sync-specific validation that rejects main/master
+	if err := ValidateSyncBranchName(branch); err != nil {
 		return err
 	}
 
diff --git a/internal/syncbranch/syncbranch_test.go b/internal/syncbranch/syncbranch_test.go
index 7c69e9dc..67fff330 100644
--- a/internal/syncbranch/syncbranch_test.go
+++ b/internal/syncbranch/syncbranch_test.go
@@ -48,6 +48,36 @@ func TestValidateBranchName(t *testing.T) {
 	}
 }
 
+func TestValidateSyncBranchName(t *testing.T) {
+	tests := []struct {
+		name    string
+		branch  string
+		wantErr bool
+	}{
+		// Valid sync branches
+		{"beads-sync is valid", "beads-sync", false},
+		{"feature branch is valid", "feature-branch", false},
+		{"empty is valid", "", false},
+
+		// GH#807: main and master should be rejected for sync branch
+		{"main is invalid for sync", "main", true},
+		{"master is invalid for sync", "master", true},
+
+		// Standard branch name validation still applies
+		{"invalid: HEAD", "HEAD", true},
+		{"invalid: contains ..", "feature..branch", true},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			err := ValidateSyncBranchName(tt.branch)
+			if (err != nil) != tt.wantErr {
+				t.Errorf("ValidateSyncBranchName(%q) error = %v, wantErr %v", tt.branch, err, tt.wantErr)
+			}
+		})
+	}
+}
+
 func newTestStore(t *testing.T) *sqlite.SQLiteStorage {
 	t.Helper()
 	store, err := sqlite.New(context.Background(), "file::memory:?mode=memory&cache=private")