diff --git a/cmd/bd/autoimport.go b/cmd/bd/autoimport.go
index c0775d0a..1d2d6b34 100644
--- a/cmd/bd/autoimport.go
+++ b/cmd/bd/autoimport.go
@@ -21,13 +21,20 @@ import (
 	"gopkg.in/yaml.v3"
 )
 
-// readFromGitRef reads file content from a git ref (branch or commit).
+// readFromGitRef reads file content from a git ref (branch or commit) in the beads repo.
 // Returns the raw bytes from git show <ref>:<path>.
 // The filePath is automatically converted to forward slashes for Windows compatibility.
 // Returns nil, err if the git command fails (e.g., file not found in ref).
+// GH#1110: Now uses RepoContext to ensure git commands run in beads repo.
 func readFromGitRef(filePath, gitRef string) ([]byte, error) {
 	gitPath := filepath.ToSlash(filePath)
-	cmd := exec.Command("git", "show", fmt.Sprintf("%s:%s", gitRef, gitPath)) // #nosec G204 - git command with safe args
+	var cmd *exec.Cmd
+	if rc, err := beads.GetRepoContext(); err == nil {
+		cmd = rc.GitCmd(context.Background(), "show", fmt.Sprintf("%s:%s", gitRef, gitPath))
+	} else {
+		// Fallback to CWD for tests or repos without beads
+		cmd = exec.Command("git", "show", fmt.Sprintf("%s:%s", gitRef, gitPath)) // #nosec G204 - git command with safe args
+	}
 	output, err := cmd.Output()
 	if err != nil {
 		return nil, fmt.Errorf("failed to read from git: %w", err)
@@ -135,8 +142,14 @@ func checkGitForIssues() (int, string, string) {
 		// Check if the sync branch exists (locally or on remote)
 		// Try origin/<branch> first (more likely to exist in fresh clones),
 		// then local <branch>
+		// GH#1110: Use RepoContext to ensure we check the beads repo
 		for _, ref := range []string{"origin/" + syncBranch, syncBranch} {
-			cmd := exec.Command("git", "rev-parse", "--verify", "--quiet", ref) // #nosec G204
+			var cmd *exec.Cmd
+			if rc, err := beads.GetRepoContext(); err == nil {
+				cmd = rc.GitCmd(context.Background(), "rev-parse", "--verify", "--quiet", ref)
+			} else {
+				cmd = exec.Command("git", "rev-parse", "--verify", "--quiet", ref) // #nosec G204
+			}
 			if err := cmd.Run(); err == nil {
 				gitRef = ref
 				break
diff --git a/cmd/bd/import.go b/cmd/bd/import.go
index b132a36b..ddf8bf8e 100644
--- a/cmd/bd/import.go
+++ b/cmd/bd/import.go
@@ -14,6 +14,7 @@ import (
 	"time"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/debug"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
@@ -635,20 +636,27 @@ func countLinesInGitHEAD(filePath string, workDir string) int {
 	return lines
 }
 
-// attemptAutoMerge attempts to resolve git conflicts using bd merge 3-way merge
+// attemptAutoMerge attempts to resolve git conflicts using bd merge 3-way merge.
+// GH#1110: Now uses RepoContext to ensure we operate on the beads repo.
 func attemptAutoMerge(conflictedPath string) error {
 	// Validate inputs
 	if conflictedPath == "" {
 		return fmt.Errorf("no file path provided for merge")
 	}
 
-	// Get git repository root
-	gitRootCmd := exec.Command("git", "rev-parse", "--show-toplevel") // #nosec G204 -- fixed git invocation for repo root discovery
-	gitRootOutput, err := gitRootCmd.Output()
-	if err != nil {
-		return fmt.Errorf("not in a git repository: %w", err)
+	// Get git repository root from RepoContext
+	var gitRoot string
+	if rc, err := beads.GetRepoContext(); err == nil {
+		gitRoot = rc.RepoRoot
+	} else {
+		// Fallback to CWD-based lookup
+		gitRootCmd := exec.Command("git", "rev-parse", "--show-toplevel") // #nosec G204 -- fixed git invocation for repo root discovery
+		gitRootOutput, err := gitRootCmd.Output()
+		if err != nil {
+			return fmt.Errorf("not in a git repository: %w", err)
+		}
+		gitRoot = strings.TrimSpace(string(gitRootOutput))
 	}
-	gitRoot := strings.TrimSpace(string(gitRootOutput))
 
 	// Convert conflicted path to absolute path relative to git root
 	absConflictedPath := conflictedPath
diff --git a/cmd/bd/reinit_test.go b/cmd/bd/reinit_test.go
index 5f2bdb7d..404baab8 100644
--- a/cmd/bd/reinit_test.go
+++ b/cmd/bd/reinit_test.go
@@ -9,6 +9,7 @@ import (
 	"runtime"
 	"testing"
 
+	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/git"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
@@ -41,6 +42,7 @@ func TestDatabaseReinitialization(t *testing.T) {
 
 // testFreshCloneAutoImport verifies auto-import works on fresh clone
 func testFreshCloneAutoImport(t *testing.T) {
+	beads.ResetCaches() // Reset cached RepoContext between subtests
 	dir := t.TempDir()
 
 	// Initialize git repo
@@ -124,6 +126,7 @@ func testFreshCloneAutoImport(t *testing.T) {
 
 // testDatabaseRemovalScenario tests the primary bug scenario
 func testDatabaseRemovalScenario(t *testing.T) {
+	beads.ResetCaches() // Reset cached RepoContext between subtests
 	dir := t.TempDir()
 
 	// Initialize git repo
@@ -225,6 +228,7 @@ func testDatabaseRemovalScenario(t *testing.T) {
 
 // testLegacyFilenameSupport tests issues.jsonl fallback
 func testLegacyFilenameSupport(t *testing.T) {
+	beads.ResetCaches() // Reset cached RepoContext between subtests
 	dir := t.TempDir()
 
 	// Initialize git repo
@@ -303,6 +307,7 @@ func testLegacyFilenameSupport(t *testing.T) {
 
 // testPrecedenceTest verifies issues.jsonl is preferred over beads.jsonl
 func testPrecedenceTest(t *testing.T) {
+	beads.ResetCaches() // Reset cached RepoContext between subtests
 	dir := t.TempDir()
 
 	// Initialize git repo
@@ -358,6 +363,7 @@ func testPrecedenceTest(t *testing.T) {
 
 // testInitSafetyCheck tests the safety check that prevents silent data loss
 func testInitSafetyCheck(t *testing.T) {
+	beads.ResetCaches() // Reset cached RepoContext between subtests
 	dir := t.TempDir()
 
 	// Initialize git repo
diff --git a/cmd/bd/status.go b/cmd/bd/status.go
index c82fc937..e8c4902e 100644
--- a/cmd/bd/status.go
+++ b/cmd/bd/status.go
@@ -2,6 +2,7 @@ package main
 
 import (
 	"bufio"
+	"context"
 	"encoding/json"
 	"fmt"
 	"os"
@@ -10,6 +11,7 @@ import (
 	"time"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/types"
 	"github.com/steveyegge/beads/internal/ui"
 )
@@ -178,7 +180,8 @@ Examples:
 	},
 }
 
-// getGitActivity calculates activity stats from git log of issues.jsonl
+// getGitActivity calculates activity stats from git log of issues.jsonl.
+// GH#1110: Now uses RepoContext to ensure git commands run in beads repo.
 func getGitActivity(hours int) *RecentActivitySummary {
 	activity := &RecentActivitySummary{
 		HoursTracked: hours,
@@ -186,7 +189,12 @@ func getGitActivity(hours int) *RecentActivitySummary {
 
 	// Run git log to get patches for the last N hours
 	since := fmt.Sprintf("%d hours ago", hours)
-	cmd := exec.Command("git", "log", "--since="+since, "--numstat", "--pretty=format:%H", ".beads/issues.jsonl") // #nosec G204 -- bounded arguments for local git history inspection
+	var cmd *exec.Cmd
+	if rc, err := beads.GetRepoContext(); err == nil {
+		cmd = rc.GitCmd(context.Background(), "log", "--since="+since, "--numstat", "--pretty=format:%H", ".beads/issues.jsonl")
+	} else {
+		cmd = exec.Command("git", "log", "--since="+since, "--numstat", "--pretty=format:%H", ".beads/issues.jsonl") // #nosec G204 -- bounded arguments for local git history inspection
+	}
 
 	output, err := cmd.Output()
 	if err != nil {
@@ -222,7 +230,11 @@ func getGitActivity(hours int) *RecentActivitySummary {
 	}
 
 	// Get detailed diff to analyze changes
-	cmd = exec.Command("git", "log", "--since="+since, "-p", ".beads/issues.jsonl") // #nosec G204 -- bounded arguments for local git history inspection
+	if rc, err := beads.GetRepoContext(); err == nil {
+		cmd = rc.GitCmd(context.Background(), "log", "--since="+since, "-p", ".beads/issues.jsonl")
+	} else {
+		cmd = exec.Command("git", "log", "--since="+since, "-p", ".beads/issues.jsonl") // #nosec G204 -- bounded arguments for local git history inspection
+	}
 	output, err = cmd.Output()
 	if err != nil {
 		return nil
diff --git a/cmd/bd/sync_branch.go b/cmd/bd/sync_branch.go
index c988539a..5d865b12 100644
--- a/cmd/bd/sync_branch.go
+++ b/cmd/bd/sync_branch.go
@@ -8,13 +8,22 @@ import (
 	"strings"
 	"time"
 
+	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
-// getCurrentBranch returns the name of the current git branch
+// getCurrentBranch returns the name of the current git branch in the beads repo.
 // Uses symbolic-ref instead of rev-parse to work in fresh repos without commits (bd-flil)
+// GH#1110: Now uses RepoContext to ensure we query the beads repo, not CWD.
+// Falls back to CWD-based query if no beads context found (for tests/standalone git).
 func getCurrentBranch(ctx context.Context) (string, error) {
-	cmd := exec.CommandContext(ctx, "git", "symbolic-ref", "--short", "HEAD")
+	var cmd *exec.Cmd
+	if rc, err := beads.GetRepoContext(); err == nil {
+		cmd = rc.GitCmd(ctx, "symbolic-ref", "--short", "HEAD")
+	} else {
+		// Fallback to CWD for tests or repos without beads
+		cmd = exec.CommandContext(ctx, "git", "symbolic-ref", "--short", "HEAD")
+	}
 	output, err := cmd.Output()
 	if err != nil {
 		return "", fmt.Errorf("failed to get current branch: %w", err)
@@ -53,12 +62,18 @@ func getSyncBranch(ctx context.Context) (string, error) {
 	return syncBranch, nil
 }
 
-// showSyncStatus shows the diff between sync branch and main branch
+// showSyncStatus shows the diff between sync branch and main branch.
+// GH#1110: Now uses RepoContext to ensure git commands run in beads repo.
 func showSyncStatus(ctx context.Context) error {
 	if !isGitRepo() {
 		return fmt.Errorf("not in a git repository")
 	}
 
+	rc, err := beads.GetRepoContext()
+	if err != nil {
+		return fmt.Errorf("failed to get repo context: %w", err)
+	}
+
 	currentBranch := getCurrentBranchOrHEAD(ctx)
 
 	syncBranch, err := getSyncBranch(ctx)
@@ -67,7 +82,7 @@ func showSyncStatus(ctx context.Context) error {
 	}
 
 	// Check if sync branch exists
-	checkCmd := exec.CommandContext(ctx, "git", "show-ref", "--verify", "--quiet", "refs/heads/"+syncBranch) //nolint:gosec // syncBranch from config
+	checkCmd := rc.GitCmd(ctx, "show-ref", "--verify", "--quiet", "refs/heads/"+syncBranch)
 	if err := checkCmd.Run(); err != nil {
 		return fmt.Errorf("sync branch '%s' does not exist", syncBranch)
 	}
@@ -77,7 +92,7 @@ func showSyncStatus(ctx context.Context) error {
 
 	// Show commit diff
 	fmt.Println("Commits in sync branch not in main:")
-	logCmd := exec.CommandContext(ctx, "git", "log", "--oneline", currentBranch+".."+syncBranch) //nolint:gosec // branch names from git
+	logCmd := rc.GitCmd(ctx, "log", "--oneline", currentBranch+".."+syncBranch)
 	logOutput, err := logCmd.CombinedOutput()
 	if err != nil {
 		return fmt.Errorf("failed to get commit log: %w\n%s", err, logOutput)
@@ -90,7 +105,7 @@ func showSyncStatus(ctx context.Context) error {
 	}
 
 	fmt.Println("\nCommits in main not in sync branch:")
-	logCmd = exec.CommandContext(ctx, "git", "log", "--oneline", syncBranch+".."+currentBranch) //nolint:gosec // branch names from git
+	logCmd = rc.GitCmd(ctx, "log", "--oneline", syncBranch+".."+currentBranch)
 	logOutput, err = logCmd.CombinedOutput()
 	if err != nil {
 		return fmt.Errorf("failed to get commit log: %w\n%s", err, logOutput)
@@ -104,7 +119,7 @@ func showSyncStatus(ctx context.Context) error {
 
 	// Show file diff for .beads/issues.jsonl
 	fmt.Println("\nFile differences in .beads/issues.jsonl:")
-	diffCmd := exec.CommandContext(ctx, "git", "diff", currentBranch+"..."+syncBranch, "--", ".beads/issues.jsonl") //nolint:gosec // branch names from git
+	diffCmd := rc.GitCmd(ctx, "diff", currentBranch+"..."+syncBranch, "--", ".beads/issues.jsonl")
 	diffOutput, err := diffCmd.CombinedOutput()
 	if err != nil {
 		// diff returns non-zero when there are differences, which is fine
@@ -122,12 +137,18 @@ func showSyncStatus(ctx context.Context) error {
 	return nil
 }
 
-// mergeSyncBranch merges the sync branch back to the main branch
+// mergeSyncBranch merges the sync branch back to the main branch.
+// GH#1110: Now uses RepoContext to ensure git commands run in beads repo.
 func mergeSyncBranch(ctx context.Context, dryRun bool) error {
 	if !isGitRepo() {
 		return fmt.Errorf("not in a git repository")
 	}
 
+	rc, err := beads.GetRepoContext()
+	if err != nil {
+		return fmt.Errorf("failed to get repo context: %w", err)
+	}
+
 	currentBranch, err := getCurrentBranch(ctx)
 	if err != nil {
 		return err
@@ -139,13 +160,13 @@ func mergeSyncBranch(ctx context.Context, dryRun bool) error {
 	}
 
 	// Check if sync branch exists
-	checkCmd := exec.CommandContext(ctx, "git", "show-ref", "--verify", "--quiet", "refs/heads/"+syncBranch) //nolint:gosec // syncBranch from config
+	checkCmd := rc.GitCmd(ctx, "show-ref", "--verify", "--quiet", "refs/heads/"+syncBranch)
 	if err := checkCmd.Run(); err != nil {
 		return fmt.Errorf("sync branch '%s' does not exist", syncBranch)
 	}
 
 	// Check if there are uncommitted changes
-	statusCmd := exec.CommandContext(ctx, "git", "status", "--porcelain")
+	statusCmd := rc.GitCmd(ctx, "status", "--porcelain")
 	statusOutput, err := statusCmd.Output()
 	if err != nil {
 		return fmt.Errorf("failed to check git status: %w", err)
@@ -159,7 +180,7 @@ func mergeSyncBranch(ctx context.Context, dryRun bool) error {
 	if dryRun {
 		fmt.Println("→ [DRY RUN] Would merge sync branch")
 		// Show what would be merged
-		logCmd := exec.CommandContext(ctx, "git", "log", "--oneline", currentBranch+".."+syncBranch) //nolint:gosec // branch names from git
+		logCmd := rc.GitCmd(ctx, "log", "--oneline", currentBranch+".."+syncBranch)
 		logOutput, _ := logCmd.CombinedOutput()
 		if len(strings.TrimSpace(string(logOutput))) > 0 {
 			fmt.Println("\nCommits that would be merged:")
@@ -171,7 +192,7 @@ func mergeSyncBranch(ctx context.Context, dryRun bool) error {
 	}
 
 	// Perform the merge
-	mergeCmd := exec.CommandContext(ctx, "git", "merge", syncBranch, "-m", fmt.Sprintf("Merge sync branch '%s'", syncBranch)) //nolint:gosec // syncBranch from config
+	mergeCmd := rc.GitCmd(ctx, "merge", syncBranch, "-m", fmt.Sprintf("Merge sync branch '%s'", syncBranch))
 	mergeOutput, err := mergeCmd.CombinedOutput()
 	if err != nil {
 		return fmt.Errorf("merge failed: %w\n%s", err, mergeOutput)
diff --git a/cmd/bd/sync_check.go b/cmd/bd/sync_check.go
index 20defcb5..3cb029b9 100644
--- a/cmd/bd/sync_check.go
+++ b/cmd/bd/sync_check.go
@@ -11,6 +11,7 @@ import (
 	"strings"
 	"time"
 
+	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/syncbranch"
 	"github.com/steveyegge/beads/internal/types"
 )
@@ -112,12 +113,20 @@ func showSyncIntegrityCheck(ctx context.Context, jsonlPath string) {
 
 // checkForcedPush detects if the sync branch has diverged from remote.
 // This can happen when someone force-pushes to the sync branch.
+// GH#1110: Now uses RepoContext to ensure git commands run in beads repo.
 func checkForcedPush(ctx context.Context) *ForcedPushCheck {
 	result := &ForcedPushCheck{
 		Detected: false,
 		Message:  "No sync branch configured or no remote",
 	}
 
+	// Get RepoContext for beads repo
+	rc, err := beads.GetRepoContext()
+	if err != nil {
+		result.Message = fmt.Sprintf("Failed to get repo context: %v", err)
+		return result
+	}
+
 	// Get sync branch name
 	if err := ensureStoreActive(); err != nil {
 		return result
@@ -129,14 +138,14 @@ func checkForcedPush(ctx context.Context) *ForcedPushCheck {
 	}
 
 	// Check if sync branch exists locally
-	checkLocalCmd := exec.CommandContext(ctx, "git", "show-ref", "--verify", "--quiet", "refs/heads/"+syncBranch) //nolint:gosec // syncBranch from config
+	checkLocalCmd := rc.GitCmd(ctx, "show-ref", "--verify", "--quiet", "refs/heads/"+syncBranch)
 	if checkLocalCmd.Run() != nil {
 		result.Message = fmt.Sprintf("Sync branch '%s' does not exist locally", syncBranch)
 		return result
 	}
 
 	// Get local ref
-	localRefCmd := exec.CommandContext(ctx, "git", "rev-parse", syncBranch) //nolint:gosec // syncBranch from config
+	localRefCmd := rc.GitCmd(ctx, "rev-parse", syncBranch)
 	localRefOutput, err := localRefCmd.Output()
 	if err != nil {
 		result.Message = "Failed to get local sync branch ref"
@@ -152,7 +161,7 @@ func checkForcedPush(ctx context.Context) *ForcedPushCheck {
 	}
 
 	// Get remote ref
-	remoteRefCmd := exec.CommandContext(ctx, "git", "rev-parse", remote+"/"+syncBranch) //nolint:gosec // remote and syncBranch from config
+	remoteRefCmd := rc.GitCmd(ctx, "rev-parse", remote+"/"+syncBranch)
 	remoteRefOutput, err := remoteRefCmd.Output()
 	if err != nil {
 		result.Message = fmt.Sprintf("Remote tracking branch '%s/%s' does not exist", remote, syncBranch)
@@ -168,14 +177,14 @@ func checkForcedPush(ctx context.Context) *ForcedPushCheck {
 	}
 
 	// Check if local is ahead of remote (normal case)
-	aheadCmd := exec.CommandContext(ctx, "git", "merge-base", "--is-ancestor", remoteRef, localRef) //nolint:gosec // refs from git rev-parse
+	aheadCmd := rc.GitCmd(ctx, "merge-base", "--is-ancestor", remoteRef, localRef)
 	if aheadCmd.Run() == nil {
 		result.Message = "Local sync branch is ahead of remote (normal)"
 		return result
 	}
 
 	// Check if remote is ahead of local (behind, needs pull)
-	behindCmd := exec.CommandContext(ctx, "git", "merge-base", "--is-ancestor", localRef, remoteRef) //nolint:gosec // refs from git rev-parse
+	behindCmd := rc.GitCmd(ctx, "merge-base", "--is-ancestor", localRef, remoteRef)
 	if behindCmd.Run() == nil {
 		result.Message = "Local sync branch is behind remote (needs pull)"
 		return result
diff --git a/cmd/bd/sync_import.go b/cmd/bd/sync_import.go
index 859a7b3d..95c830fe 100644
--- a/cmd/bd/sync_import.go
+++ b/cmd/bd/sync_import.go
@@ -9,6 +9,7 @@ import (
 	"os/exec"
 	"time"
 
+	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/debug"
 	"github.com/steveyegge/beads/internal/types"
 )
@@ -162,6 +163,7 @@ func resolveNoGitHistoryForFromMain(fromMain, noGitHistory bool) bool {
 // This fetches beads from main and imports them, discarding local beads changes.
 // If sync.remote is configured (e.g., "upstream" for fork workflows), uses that remote
 // instead of "origin".
+// GH#1110: Now uses RepoContext to ensure git commands run in beads repo.
 func doSyncFromMain(ctx context.Context, jsonlPath string, renameOnImport bool, dryRun bool, noGitHistory bool) error {
 	// Determine which remote to use (default: origin, but can be configured via sync.remote)
 	remote := "origin"
@@ -190,8 +192,14 @@ func doSyncFromMain(ctx context.Context, jsonlPath string, renameOnImport bool,
 		return fmt.Errorf("no git remote configured")
 	}
 
+	// Get RepoContext for beads repo
+	rc, err := beads.GetRepoContext()
+	if err != nil {
+		return fmt.Errorf("failed to get repo context: %w", err)
+	}
+
 	// Verify the configured remote exists
-	checkRemoteCmd := exec.CommandContext(ctx, "git", "remote", "get-url", remote)
+	checkRemoteCmd := rc.GitCmd(ctx, "remote", "get-url", remote)
 	if err := checkRemoteCmd.Run(); err != nil {
 		return fmt.Errorf("configured sync.remote '%s' does not exist (run 'git remote add %s <url>')", remote, remote)
 	}
@@ -200,14 +208,14 @@ func doSyncFromMain(ctx context.Context, jsonlPath string, renameOnImport bool,
 
 	// Step 1: Fetch from main
 	fmt.Printf("→ Fetching from %s/%s...\n", remote, defaultBranch)
-	fetchCmd := exec.CommandContext(ctx, "git", "fetch", remote, defaultBranch) //nolint:gosec // remote and defaultBranch from config
+	fetchCmd := rc.GitCmd(ctx, "fetch", remote, defaultBranch)
 	if output, err := fetchCmd.CombinedOutput(); err != nil {
 		return fmt.Errorf("git fetch %s %s failed: %w\n%s", remote, defaultBranch, err, output)
 	}
 
 	// Step 2: Checkout .beads/ directory from main
 	fmt.Printf("→ Checking out beads from %s/%s...\n", remote, defaultBranch)
-	checkoutCmd := exec.CommandContext(ctx, "git", "checkout", fmt.Sprintf("%s/%s", remote, defaultBranch), "--", ".beads/") //nolint:gosec // remote and defaultBranch from config
+	checkoutCmd := rc.GitCmd(ctx, "checkout", fmt.Sprintf("%s/%s", remote, defaultBranch), "--", ".beads/")
 	if output, err := checkoutCmd.CombinedOutput(); err != nil {
 		return fmt.Errorf("git checkout .beads/ from %s/%s failed: %w\n%s", remote, defaultBranch, err, output)
 	}