diff --git a/internal/session/storage.go b/internal/session/storage.go
index d793355f..4e4d0e00 100644
--- a/internal/session/storage.go
+++ b/internal/session/storage.go
@@ -728,7 +728,7 @@ func (s *Storage) convertToInstances(data *StorageData) ([]*Instance, []*GroupDa
 			// Pass instance ID for activity hooks (enables real-time status updates)
 			tmuxSess.InstanceID = instData.ID
 			tmuxSess.SetInjectStatusLine(GetTmuxSettings().GetInjectStatusLine())
-			// Note: EnableMouseMode is now deferred to EnsureConfigured()
+			// Note: EnableMouseMode and ConfigureStatusBar are deferred to EnsureConfigured()
 			// Called automatically when user attaches to session
 		}
 
@@ -792,6 +792,12 @@ func (s *Storage) convertToInstances(data *StorageData) ([]*Instance, []*GroupDa
 			})
 		}
 
+		// Set tmux option overrides so EnsureConfigured/ConfigureStatusBar
+		// respects user-defined keys (e.g. status = "2" for multi-line bar).
+		if tmuxSess != nil {
+			tmuxSess.OptionOverrides = inst.buildTmuxOptionOverrides()
+		}
+
 		// PERFORMANCE: Skip UpdateStatus at load time - use cached status from SQLite
 		// The background worker will update status on first tick.
 		// This saves one subprocess call per session at startup.
diff --git a/internal/session/userconfig.go b/internal/session/userconfig.go
index 1c15cd6b..18cdd1e2 100644
--- a/internal/session/userconfig.go
+++ b/internal/session/userconfig.go
@@ -1730,7 +1730,12 @@ auto_cleanup = true
 # Default: true (agent-deck injects its own status bar with session info)
 # inject_status_line = false
 # Override tmux options applied to every session (applied after defaults)
+# Options matching agent-deck's managed keys (status, status-style,
+# status-left-length, status-right, status-right-length) will cause agent-deck
+# to skip its default for that key, letting your value take full effect.
 # options = { "allow-passthrough" = "all", "history-limit" = "50000" }
+# Example: keep agent-deck notifications but use a 2-line status bar
+# options = { "status" = "2" }
 
 # ============================================================================
 # MCP Server Definitions
diff --git a/internal/tmux/tmux.go b/internal/tmux/tmux.go
index 45c7f718..23c9dbce 100644
--- a/internal/tmux/tmux.go
+++ b/internal/tmux/tmux.go
@@ -1347,29 +1347,56 @@ func (s *Session) IsPaneDead() bool {
 	return strings.TrimSpace(string(out)) == "1"
 }
 
-// ConfigureStatusBar sets up the tmux status bar with session info
-// Shows: notification bar on left (managed by NotificationManager), session info on right
-// NOTE: status-left is reserved for the notification bar showing waiting sessions
-// This function only configures status-right to avoid overwriting notification bar
-func (s *Session) ConfigureStatusBar() {
-	// Skip status bar injection if disabled by user config
+// buildStatusBarArgs returns the tmux command args for configuring the status bar.
+// Returns nil if status bar injection is disabled.
+// Skips any option key that exists in s.OptionOverrides — user-defined options take precedence.
+func (s *Session) buildStatusBarArgs() []string {
 	if !s.injectStatusLine {
-		return
+		return nil
 	}
 	themeStyle := currentTmuxThemeStyle()
 	rightStatus := s.themedStatusRight(themeStyle)
 
-	// PERFORMANCE: Batch all 5 status bar options into single subprocess call
-	// Uses tmux command chaining with \; separator (73% reduction in subprocess calls)
-	// Before: 5 separate exec.Command calls = 5 subprocess spawns
-	// After: 1 exec.Command call = 1 subprocess spawn
-	cmd := exec.Command("tmux",
-		"set-option", "-t", s.Name, "status", "on", ";",
-		"set-option", "-t", s.Name, "status-style", themeStyle.statusStyle, ";",
-		"set-option", "-t", s.Name, "status-left-length", "120", ";",
-		"set-option", "-t", s.Name, "status-right", rightStatus, ";",
-		"set-option", "-t", s.Name, "status-right-length", "80")
-	_ = cmd.Run()
+	// Managed defaults — each can be skipped if user defined it in [tmux] options
+	type option struct {
+		key   string
+		value string
+	}
+	defaults := []option{
+		{"status", "on"},
+		{"status-style", themeStyle.statusStyle},
+		{"status-left-length", "120"},
+		{"status-right", rightStatus},
+		{"status-right-length", "80"},
+	}
+
+	var args []string
+	for _, opt := range defaults {
+		if _, overridden := s.OptionOverrides[opt.key]; overridden {
+			continue
+		}
+		if len(args) > 0 {
+			args = append(args, ";")
+		}
+		args = append(args, "set-option", "-t", s.Name, opt.key, opt.value)
+	}
+
+	if len(args) == 0 {
+		return nil
+	}
+	return args
+}
+
+// ConfigureStatusBar sets up the tmux status bar with session info.
+// Shows: notification bar on left (managed by NotificationManager), session info on right.
+// NOTE: status-left is reserved for the notification bar showing waiting sessions.
+// Options defined in [tmux] options are respected — agent-deck skips those keys.
+func (s *Session) ConfigureStatusBar() {
+	args := s.buildStatusBarArgs()
+	if args == nil {
+		return
+	}
+	_ = exec.Command("tmux", args...).Run()
 }
 
 // EnableMouseMode enables mouse scrolling, clipboard integration, and optimal settings
diff --git a/internal/tmux/tmux_test.go b/internal/tmux/tmux_test.go
index 1ef8f4d8..15267bad 100644
--- a/internal/tmux/tmux_test.go
+++ b/internal/tmux/tmux_test.go
@@ -2552,3 +2552,130 @@ func TestParseWindowCacheEmptyInput(t *testing.T) {
 	assert.Empty(t, sessionCache)
 	assert.Empty(t, windowCache)
 }
+
+func TestBuildStatusBarArgs(t *testing.T) {
+	tests := []struct {
+		name            string
+		sessionName     string
+		displayName     string
+		workDir         string
+		optionOverrides map[string]string
+		wantKeys        []string // keys that SHOULD appear in args
+		skipKeys        []string // keys that should NOT appear in args
+	}{
+		{
+			name:            "no overrides - all defaults applied",
+			sessionName:     "test-sess",
+			displayName:     "my-project",
+			workDir:         "/home/user/my-project",
+			optionOverrides: nil,
+			wantKeys:        []string{"status", "status-style", "status-left-length", "status-right", "status-right-length"},
+			skipKeys:        nil,
+		},
+		{
+			name:            "empty overrides - all defaults applied",
+			sessionName:     "test-sess",
+			displayName:     "my-project",
+			workDir:         "/home/user/my-project",
+			optionOverrides: map[string]string{},
+			wantKeys:        []string{"status", "status-style", "status-left-length", "status-right", "status-right-length"},
+			skipKeys:        nil,
+		},
+		{
+			name:            "status overridden - status skipped",
+			sessionName:     "test-sess",
+			displayName:     "my-project",
+			workDir:         "/home/user/my-project",
+			optionOverrides: map[string]string{"status": "2"},
+			wantKeys:        []string{"status-style", "status-left-length", "status-right", "status-right-length"},
+			skipKeys:        []string{"status"},
+		},
+		{
+			name:            "status-style overridden - status-style skipped",
+			sessionName:     "test-sess",
+			displayName:     "my-project",
+			workDir:         "/home/user/my-project",
+			optionOverrides: map[string]string{"status-style": "bg=#000000"},
+			wantKeys:        []string{"status", "status-left-length", "status-right", "status-right-length"},
+			skipKeys:        []string{"status-style"},
+		},
+		{
+			name:            "multiple overrides - multiple skipped",
+			sessionName:     "test-sess",
+			displayName:     "my-project",
+			workDir:         "/home/user/my-project",
+			optionOverrides: map[string]string{"status": "2", "status-style": "bg=#000", "status-right-length": "100"},
+			wantKeys:        []string{"status-left-length", "status-right"},
+			skipKeys:        []string{"status", "status-style", "status-right-length"},
+		},
+		{
+			name:            "unrelated override - all defaults applied",
+			sessionName:     "test-sess",
+			displayName:     "my-project",
+			workDir:         "/home/user/my-project",
+			optionOverrides: map[string]string{"history-limit": "50000"},
+			wantKeys:        []string{"status", "status-style", "status-left-length", "status-right", "status-right-length"},
+			skipKeys:        nil,
+		},
+		{
+			name:        "all managed keys overridden - returns nil",
+			sessionName: "test-sess",
+			displayName: "my-project",
+			workDir:     "/home/user/my-project",
+			optionOverrides: map[string]string{
+				"status": "2", "status-style": "bg=#000",
+				"status-left-length": "50", "status-right": "custom",
+				"status-right-length": "100",
+			},
+			wantKeys: nil,
+			skipKeys: nil,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			s := &Session{
+				Name:             tt.sessionName,
+				DisplayName:      tt.displayName,
+				WorkDir:          tt.workDir,
+				OptionOverrides:  tt.optionOverrides,
+				injectStatusLine: true,
+			}
+			args := s.buildStatusBarArgs()
+
+			if tt.wantKeys == nil && tt.skipKeys == nil {
+				assert.Nil(t, args, "args should be nil when all managed keys are overridden")
+				return
+			}
+
+			require.NotNil(t, args, "args should not be nil when injectStatusLine is true")
+
+			// Extract the set of option keys from the args.
+			// Args follow the pattern: "set-option" "-t" <session> <key> <value> [";"]
+			keys := make(map[string]bool)
+			for i, a := range args {
+				if a == "set-option" && i+3 < len(args) {
+					keys[args[i+3]] = true
+				}
+			}
+
+			for _, key := range tt.wantKeys {
+				assert.True(t, keys[key], "expected key %q in args", key)
+			}
+			for _, key := range tt.skipKeys {
+				assert.False(t, keys[key], "key %q should be skipped", key)
+			}
+		})
+	}
+}
+
+func TestBuildStatusBarArgs_InjectDisabled(t *testing.T) {
+	s := &Session{
+		Name:             "test-sess",
+		DisplayName:      "proj",
+		WorkDir:          "/tmp",
+		injectStatusLine: false,
+	}
+	args := s.buildStatusBarArgs()
+	assert.Nil(t, args, "args should be nil when injectStatusLine is false")
+}