diff --git a/internal/app/app.go b/internal/app/app.go
index 50247b165aea1ccc6df378d0d1d3241b9526388e..b798dd789daba8fe7f227a3435293674ba4bff85 100644
--- a/internal/app/app.go
+++ b/internal/app/app.go
@@ -59,7 +59,7 @@ func New(ctx context.Context, conn *sql.DB, cfg *config.Config) (*App, error) {
 	sessions := session.NewService(q)
 	messages := message.NewService(q)
 	files := history.NewService(q, conn)
-	skipPermissionsRequests := cfg.Options != nil && cfg.Options.SkipPermissionsRequests
+	skipPermissionsRequests := cfg.Permissions != nil && cfg.Permissions.SkipRequests
 	allowedCommands := []string{}
 	if cfg.Permissions != nil && cfg.Permissions.AllowedTools != nil {
 		allowedCommands = cfg.Permissions.AllowedTools
diff --git a/internal/cmd/root.go b/internal/cmd/root.go
index d63160992141da26b6a26610b06f1b601213e00d..254cf340205d7da54984b291c0f88f8a130af80d 100644
--- a/internal/cmd/root.go
+++ b/internal/cmd/root.go
@@ -73,7 +73,10 @@ to assist developers in writing, debugging, and understanding code directly from
 		if err != nil {
 			return err
 		}
-		cfg.Options.SkipPermissionsRequests = yolo
+		if cfg.Permissions == nil {
+			cfg.Permissions = &config.Permissions{}
+		}
+		cfg.Permissions.SkipRequests = yolo
 
 		ctx := cmd.Context()
 
diff --git a/internal/config/config.go b/internal/config/config.go
index 5766825a66fca67c1665074fde737b458d41e933..95fd9e509b940159950064f1ded56ffb8c66e1b2 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -122,16 +122,16 @@ type TUIOptions struct {
 
 type Permissions struct {
 	AllowedTools []string `json:"allowed_tools,omitempty"` // Tools that don't require permission prompts
+	SkipRequests bool     `json:"-"`                       // Automatically accept all permissions (YOLO mode)
 }
 
 type Options struct {
-	ContextPaths            []string    `json:"context_paths,omitempty"`
-	TUI                     *TUIOptions `json:"tui,omitempty"`
-	Debug                   bool        `json:"debug,omitempty"`
-	DebugLSP                bool        `json:"debug_lsp,omitempty"`
-	DisableAutoSummarize    bool        `json:"disable_auto_summarize,omitempty"`
-	DataDirectory           string      `json:"data_directory,omitempty"` // Relative to the cwd
-	SkipPermissionsRequests bool        `json:"-"`                        // Automatically accept all permissions (YOLO mode)
+	ContextPaths         []string    `json:"context_paths,omitempty"`
+	TUI                  *TUIOptions `json:"tui,omitempty"`
+	Debug                bool        `json:"debug,omitempty"`
+	DebugLSP             bool        `json:"debug_lsp,omitempty"`
+	DisableAutoSummarize bool        `json:"disable_auto_summarize,omitempty"`
+	DataDirectory        string      `json:"data_directory,omitempty"` // Relative to the cwd
 }
 
 type MCPs map[string]MCPConfig