diff --git a/cmd/bd/doctor.go b/cmd/bd/doctor.go
index a6ad8a94..c004083f 100644
--- a/cmd/bd/doctor.go
+++ b/cmd/bd/doctor.go
@@ -457,6 +457,11 @@ func runDiagnostics(path string) doctorResult {
 	result.Checks = append(result.Checks, orphanedIssuesCheck)
 	// Don't fail overall check for orphaned issues, just warn
 
+	// Check 17c: Sync branch gitignore flags (GH#870)
+	syncBranchGitignoreCheck := convertWithCategory(doctor.CheckSyncBranchGitignore(), doctor.CategoryGit)
+	result.Checks = append(result.Checks, syncBranchGitignoreCheck)
+	// Don't fail overall check for sync branch gitignore, just warn
+
 	// Check 18: Deletions manifest (legacy, now replaced by tombstones)
 	deletionsCheck := convertWithCategory(doctor.CheckDeletionsManifest(path), doctor.CategoryMetadata)
 	result.Checks = append(result.Checks, deletionsCheck)
diff --git a/cmd/bd/doctor/fix/sync_branch.go b/cmd/bd/doctor/fix/sync_branch.go
index e595e067..b20a1c19 100644
--- a/cmd/bd/doctor/fix/sync_branch.go
+++ b/cmd/bd/doctor/fix/sync_branch.go
@@ -2,7 +2,9 @@ package fix
 
 import (
 	"fmt"
+	"os"
 	"os/exec"
+	"path/filepath"
 	"strings"
 )
 
@@ -147,3 +149,162 @@ func SyncBranchHealth(path, syncBranch string) error {
 	fmt.Printf("  ✓ Recreated %s from %s and pushed\n", syncBranch, mainBranch)
 	return nil
 }
+
+// SyncBranchGitignore sets git index flags to hide .beads/issues.jsonl from git status
+// when sync.branch is configured. This prevents the file from showing as modified on
+// the main branch while actual data lives on the sync branch. (GH#797, GH#801, GH#870)
+//
+// Sets both flags for comprehensive hiding:
+// - assume-unchanged: Performance optimization, skips file stat check
+// - skip-worktree: Clear error message if user tries explicit `git add`
+func SyncBranchGitignore(path string) error {
+	if err := validateBeadsWorkspace(path); err != nil {
+		return err
+	}
+
+	// Find the .beads directory
+	beadsDir := filepath.Join(path, ".beads")
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		return fmt.Errorf(".beads directory not found at %s", beadsDir)
+	}
+
+	// Check if issues.jsonl exists and is tracked by git
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+	if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
+		// File doesn't exist, nothing to hide
+		return nil
+	}
+
+	// Check if file is tracked by git
+	cmd := exec.Command("git", "ls-files", "--error-unmatch", jsonlPath)
+	cmd.Dir = path
+	if err := cmd.Run(); err != nil {
+		// File is not tracked - add to .git/info/exclude instead
+		return addToGitExclude(path, ".beads/issues.jsonl")
+	}
+
+	// File is tracked - set both git index flags
+	// These must be separate commands (git quirk)
+	cmd = exec.Command("git", "update-index", "--assume-unchanged", jsonlPath)
+	cmd.Dir = path
+	if out, err := cmd.CombinedOutput(); err != nil {
+		return fmt.Errorf("failed to set assume-unchanged: %w\n%s", err, out)
+	}
+
+	cmd = exec.Command("git", "update-index", "--skip-worktree", jsonlPath)
+	cmd.Dir = path
+	if out, err := cmd.CombinedOutput(); err != nil {
+		// Revert assume-unchanged if skip-worktree fails
+		revertCmd := exec.Command("git", "update-index", "--no-assume-unchanged", jsonlPath)
+		revertCmd.Dir = path
+		_ = revertCmd.Run()
+		return fmt.Errorf("failed to set skip-worktree: %w\n%s", err, out)
+	}
+
+	fmt.Println("  ✓ Set git index flags to hide .beads/issues.jsonl")
+	return nil
+}
+
+// ClearSyncBranchGitignore removes git index flags from .beads/issues.jsonl.
+// Called when sync.branch is disabled to restore normal git tracking.
+func ClearSyncBranchGitignore(path string) error {
+	beadsDir := filepath.Join(path, ".beads")
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+
+	if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
+		return nil // File doesn't exist, nothing to do
+	}
+
+	// Check if file is tracked
+	cmd := exec.Command("git", "ls-files", "--error-unmatch", jsonlPath)
+	cmd.Dir = path
+	if err := cmd.Run(); err != nil {
+		return nil // Not tracked, nothing to clear
+	}
+
+	// Clear both flags
+	cmd = exec.Command("git", "update-index", "--no-assume-unchanged", jsonlPath)
+	cmd.Dir = path
+	_ = cmd.Run() // Ignore errors - flag might not be set
+
+	cmd = exec.Command("git", "update-index", "--no-skip-worktree", jsonlPath)
+	cmd.Dir = path
+	_ = cmd.Run() // Ignore errors - flag might not be set
+
+	return nil
+}
+
+// HasSyncBranchGitignoreFlags checks if git index flags are set on .beads/issues.jsonl
+func HasSyncBranchGitignoreFlags(path string) (bool, bool, error) {
+	beadsDir := filepath.Join(path, ".beads")
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+
+	if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
+		return false, false, nil
+	}
+
+	// Get file status from git ls-files -v
+	// 'h' = assume-unchanged, 'S' = skip-worktree
+	cmd := exec.Command("git", "ls-files", "-v", jsonlPath)
+	cmd.Dir = path
+	output, err := cmd.Output()
+	if err != nil {
+		return false, false, nil // File not tracked
+	}
+
+	line := strings.TrimSpace(string(output))
+	if len(line) == 0 {
+		return false, false, nil
+	}
+
+	// First character indicates status:
+	// 'H' = tracked, 'h' = assume-unchanged, 'S' = skip-worktree
+	firstChar := line[0]
+	hasAssumeUnchanged := firstChar == 'h'
+	hasSkipWorktree := firstChar == 'S'
+
+	return hasAssumeUnchanged, hasSkipWorktree, nil
+}
+
+// addToGitExclude adds a pattern to .git/info/exclude
+func addToGitExclude(path, pattern string) error {
+	// Get git directory
+	cmd := exec.Command("git", "rev-parse", "--git-dir")
+	cmd.Dir = path
+	output, err := cmd.Output()
+	if err != nil {
+		return fmt.Errorf("failed to get git directory: %w", err)
+	}
+
+	gitDir := strings.TrimSpace(string(output))
+	if !filepath.IsAbs(gitDir) {
+		gitDir = filepath.Join(path, gitDir)
+	}
+
+	excludePath := filepath.Join(gitDir, "info", "exclude")
+
+	// Create info directory if needed
+	if err := os.MkdirAll(filepath.Dir(excludePath), 0755); err != nil {
+		return fmt.Errorf("failed to create info directory: %w", err)
+	}
+
+	// Check if pattern already exists
+	content, _ := os.ReadFile(excludePath)
+	if strings.Contains(string(content), pattern) {
+		return nil // Already excluded
+	}
+
+	// Append pattern
+	f, err := os.OpenFile(excludePath, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0644)
+	if err != nil {
+		return fmt.Errorf("failed to open exclude file: %w", err)
+	}
+	defer f.Close()
+
+	if _, err := f.WriteString(pattern + "\n"); err != nil {
+		return fmt.Errorf("failed to write exclude pattern: %w", err)
+	}
+
+	fmt.Printf("  ✓ Added %s to .git/info/exclude\n", pattern)
+	return nil
+}
diff --git a/cmd/bd/doctor/gitignore.go b/cmd/bd/doctor/gitignore.go
index 8bf0458b..4b117575 100644
--- a/cmd/bd/doctor/gitignore.go
+++ b/cmd/bd/doctor/gitignore.go
@@ -7,6 +7,7 @@ import (
 	"path/filepath"
 	"strings"
 
+	"github.com/steveyegge/beads/cmd/bd/doctor/fix"
 	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
@@ -262,3 +263,93 @@ func FixRedirectTracking() error {
 
 	return nil
 }
+
+// CheckSyncBranchGitignore checks if git index flags are set on issues.jsonl when sync.branch is configured.
+// Without these flags, the file appears modified in git status even though changes go to the sync branch.
+// GH#797, GH#801, GH#870.
+func CheckSyncBranchGitignore() DoctorCheck {
+	// Only relevant when sync.branch is configured
+	branch := syncbranch.GetFromYAML()
+	if branch == "" {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "N/A (sync.branch not configured)",
+		}
+	}
+
+	issuesPath := filepath.Join(".beads", "issues.jsonl")
+
+	// Check if file exists
+	if _, err := os.Stat(issuesPath); os.IsNotExist(err) {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "No issues.jsonl yet",
+		}
+	}
+
+	// Check if file is tracked by git
+	cmd := exec.Command("git", "ls-files", "--error-unmatch", issuesPath) // #nosec G204 - args are hardcoded paths
+	if err := cmd.Run(); err != nil {
+		// File is not tracked - check if it's excluded
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "issues.jsonl is not tracked (via .gitignore or exclude)",
+		}
+	}
+
+	// File is tracked - check for git index flags
+	cwd, err := os.Getwd()
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusWarning,
+			Message: "Cannot determine current directory",
+		}
+	}
+
+	hasAssumeUnchanged, hasSkipWorktree, err := fix.HasSyncBranchGitignoreFlags(cwd)
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusWarning,
+			Message: "Cannot check git index flags",
+			Detail:  err.Error(),
+		}
+	}
+
+	if hasAssumeUnchanged || hasSkipWorktree {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "Git index flags set (issues.jsonl hidden from git status)",
+		}
+	}
+
+	// No flags set - this is the problem case
+	return DoctorCheck{
+		Name:    "Sync Branch Gitignore",
+		Status:  StatusWarning,
+		Message: "issues.jsonl shows as modified (missing git index flags)",
+		Detail:  fmt.Sprintf("sync.branch='%s' configured but issues.jsonl appears in git status", branch),
+		Fix:     "Run 'bd doctor --fix' or 'bd sync' to set git index flags",
+	}
+}
+
+// FixSyncBranchGitignore sets git index flags on issues.jsonl when sync.branch is configured.
+func FixSyncBranchGitignore() error {
+	// Only relevant when sync.branch is configured
+	branch := syncbranch.GetFromYAML()
+	if branch == "" {
+		return nil // Not in sync-branch mode, nothing to do
+	}
+
+	cwd, err := os.Getwd()
+	if err != nil {
+		return fmt.Errorf("cannot determine current directory: %w", err)
+	}
+
+	return fix.SyncBranchGitignore(cwd)
+}
diff --git a/cmd/bd/doctor_fix.go b/cmd/bd/doctor_fix.go
index f6ce5e1a..e127e3e6 100644
--- a/cmd/bd/doctor_fix.go
+++ b/cmd/bd/doctor_fix.go
@@ -251,6 +251,8 @@ func applyFixList(path string, fixes []doctorCheck) {
 			// No auto-fix: sync-branch should be added to config.yaml (version controlled)
 			fmt.Printf("  ⚠ Add 'sync-branch: beads-sync' to .beads/config.yaml\n")
 			continue
+		case "Sync Branch Gitignore":
+			err = doctor.FixSyncBranchGitignore()
 		case "Database Config":
 			err = fix.DatabaseConfig(path)
 		case "JSONL Config":
diff --git a/cmd/bd/sync.go b/cmd/bd/sync.go
index a94ed2bf..f01ef372 100644
--- a/cmd/bd/sync.go
+++ b/cmd/bd/sync.go
@@ -9,6 +9,7 @@ import (
 	"strings"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/cmd/bd/doctor/fix"
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/debug"
@@ -835,6 +836,15 @@ Use --merge to merge the sync branch back to main branch.`,
 					// Non-fatal - just means git status will show modified files
 					debug.Logf("sync: failed to restore .beads/ from branch: %v", err)
 				}
+
+				// GH#870: Set git index flags to hide .beads/issues.jsonl from git status.
+				// This prevents the file from appearing modified on main when using sync-branch.
+				if cwd, err := os.Getwd(); err == nil {
+					if err := fix.SyncBranchGitignore(cwd); err != nil {
+						debug.Logf("sync: failed to set gitignore flags: %v", err)
+					}
+				}
+
 				// Skip final flush in PersistentPostRun - we've already exported to sync branch
 				// and restored the working directory to match the current branch
 				skipFinalFlush = true