diff --git a/cmd/bd/doctor/gitignore.go b/cmd/bd/doctor/gitignore.go
index 0a3a90a7..8bf0458b 100644
--- a/cmd/bd/doctor/gitignore.go
+++ b/cmd/bd/doctor/gitignore.go
@@ -6,6 +6,8 @@ import (
 	"os/exec"
 	"path/filepath"
 	"strings"
+
+	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
 // GitignoreTemplate is the canonical .beads/.gitignore content
@@ -133,6 +135,7 @@ func FixGitignore() error {
 // CheckIssuesTracking verifies that issues.jsonl is tracked by git.
 // This catches cases where global gitignore patterns (e.g., *.jsonl) would
 // cause issues.jsonl to be ignored, breaking bd sync.
+// In sync-branch mode, the file may be intentionally ignored in working branches (GH#858).
 func CheckIssuesTracking() DoctorCheck {
 	issuesPath := filepath.Join(".beads", "issues.jsonl")
 
@@ -146,6 +149,17 @@ func CheckIssuesTracking() DoctorCheck {
 		}
 	}
 
+	// In sync-branch mode, JSONL files may be intentionally ignored in working branches.
+	// They are tracked only in the dedicated sync branch.
+	if branch := syncbranch.GetFromYAML(); branch != "" {
+		return DoctorCheck{
+			Name:    "Issues Tracking",
+			Status:  StatusOK,
+			Message: "N/A (sync-branch mode)",
+			Detail:  fmt.Sprintf("JSONL files tracked in '%s' branch only", branch),
+		}
+	}
+
 	// Check if git considers this file ignored
 	// git check-ignore exits 0 if ignored, 1 if not ignored, 128 if error
 	cmd := exec.Command("git", "check-ignore", "-q", issuesPath) // #nosec G204 - args are hardcoded paths
diff --git a/cmd/bd/doctor/installation.go b/cmd/bd/doctor/installation.go
index a4734049..5e6b0132 100644
--- a/cmd/bd/doctor/installation.go
+++ b/cmd/bd/doctor/installation.go
@@ -13,6 +13,7 @@ import (
 	"github.com/steveyegge/beads/cmd/bd/doctor/fix"
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/git"
+	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
 // CheckInstallation verifies that .beads directory exists
@@ -142,7 +143,9 @@ func CheckPermissions(path string) DoctorCheck {
 	}
 }
 
-// CheckUntrackedBeadsFiles checks for untracked .beads/*.jsonl files that should be committed
+// CheckUntrackedBeadsFiles checks for untracked .beads/*.jsonl files that should be committed.
+// In sync-branch mode, JSONL files are intentionally untracked in working branches
+// and only committed to the dedicated sync branch (GH#858).
 func CheckUntrackedBeadsFiles(path string) DoctorCheck {
 	beadsDir := filepath.Join(path, ".beads")
 
@@ -155,6 +158,17 @@ func CheckUntrackedBeadsFiles(path string) DoctorCheck {
 		}
 	}
 
+	// In sync-branch mode, JSONL files are intentionally untracked in working branches.
+	// They are committed only to the dedicated sync branch via bd sync.
+	if branch := syncbranch.GetFromYAML(); branch != "" {
+		return DoctorCheck{
+			Name:    "Untracked Files",
+			Status:  StatusOK,
+			Message: "N/A (sync-branch mode)",
+			Detail:  fmt.Sprintf("JSONL files tracked in '%s' branch only", branch),
+		}
+	}
+
 	// Check if we're in a git repository using worktree-aware detection
 	_, err := git.GetGitDir()
 	if err != nil {