diff --git a/packages/app/src/components/agent-status-bar.tsx b/packages/app/src/components/agent-status-bar.tsx
index 5954ad2af..cc2f22917 100644
--- a/packages/app/src/components/agent-status-bar.tsx
+++ b/packages/app/src/components/agent-status-bar.tsx
@@ -962,13 +962,14 @@ export function AgentStatusBar({ agentId, serverId, onDropdownClose }: AgentStat
           return;
         }
         void updatePreferences(
-          mergeProviderPreferences({
-            preferences,
-            provider: agent.provider,
-            updates: {
-              model: modelId,
-            },
-          }),
+          (current) =>
+            mergeProviderPreferences({
+              preferences: current,
+              provider: agent.provider,
+              updates: {
+                model: modelId,
+              },
+            }),
         ).catch((error) => {
           console.warn("[AgentStatusBar] persist model preference failed", error);
         });
@@ -978,7 +979,7 @@ export function AgentStatusBar({ agentId, serverId, onDropdownClose }: AgentStat
       }}
       favoriteKeys={favoriteKeys}
       onToggleFavoriteModel={(provider, modelId) => {
-        void updatePreferences(toggleFavoriteModel({ preferences, provider, modelId })).catch((error) => {
+        void updatePreferences((current) => toggleFavoriteModel({ preferences: current, provider, modelId })).catch((error) => {
           console.warn("[AgentStatusBar] toggle favorite model failed", error);
         });
       }}
@@ -991,16 +992,17 @@ export function AgentStatusBar({ agentId, serverId, onDropdownClose }: AgentStat
         const activeModelId = modelSelection.activeModelId;
         if (activeModelId) {
           void updatePreferences(
-            mergeProviderPreferences({
-              preferences,
-              provider: agent.provider,
-              updates: {
-                model: activeModelId,
-                thinkingByModel: {
-                  [activeModelId]: thinkingOptionId,
+            (current) =>
+              mergeProviderPreferences({
+                preferences: current,
+                provider: agent.provider,
+                updates: {
+                  model: activeModelId,
+                  thinkingByModel: {
+                    [activeModelId]: thinkingOptionId,
+                  },
                 },
-              },
-            }),
+              }),
           ).catch((error) => {
             console.warn("[AgentStatusBar] persist thinking preference failed", error);
           });
@@ -1014,6 +1016,20 @@ export function AgentStatusBar({ agentId, serverId, onDropdownClose }: AgentStat
         if (!client) {
           return;
         }
+        void updatePreferences(
+          (current) =>
+            mergeProviderPreferences({
+              preferences: current,
+              provider: agent.provider,
+              updates: {
+                featureValues: {
+                  [featureId]: value,
+                },
+              },
+            }),
+        ).catch((error) => {
+          console.warn("[AgentStatusBar] persist feature preference failed", error);
+        });
         void client.setAgentFeature(agentId, featureId, value).catch((error) => {
           console.warn("[AgentStatusBar] setAgentFeature failed", error);
         });
@@ -1083,7 +1099,7 @@ export function DraftAgentStatusBar({
           onSelect={onSelectProviderAndModel}
           favoriteKeys={favoriteKeys}
           onToggleFavorite={(provider, modelId) => {
-            void updatePreferences(toggleFavoriteModel({ preferences, provider, modelId })).catch((error) => {
+            void updatePreferences((current) => toggleFavoriteModel({ preferences: current, provider, modelId })).catch((error) => {
               console.warn("[DraftAgentStatusBar] toggle favorite model failed", error);
             });
           }}
@@ -1129,7 +1145,7 @@ export function DraftAgentStatusBar({
         isModelLoading={isAllModelsLoading}
         favoriteKeys={favoriteKeys}
         onToggleFavoriteModel={(provider, modelId) => {
-          void updatePreferences(toggleFavoriteModel({ preferences, provider, modelId })).catch((error) => {
+          void updatePreferences((current) => toggleFavoriteModel({ preferences: current, provider, modelId })).catch((error) => {
             console.warn("[DraftAgentStatusBar] toggle favorite model failed", error);
           });
         }}
diff --git a/packages/app/src/hooks/feature-preferences.test.ts b/packages/app/src/hooks/feature-preferences.test.ts
new file mode 100644
index 000000000..7cfca13a6
--- /dev/null
+++ b/packages/app/src/hooks/feature-preferences.test.ts
@@ -0,0 +1,53 @@
+import { describe, expect, it } from "vitest";
+
+import { resolveFeatureValues } from "./feature-preferences";
+
+describe("feature-preferences", () => {
+  const features = [
+    {
+      type: "toggle" as const,
+      id: "fast_mode",
+      label: "Fast",
+      value: false,
+    },
+    {
+      type: "toggle" as const,
+      id: "plan_mode",
+      label: "Plan",
+      value: false,
+    },
+  ];
+
+  it("restores persisted values for available features", () => {
+    expect(
+      resolveFeatureValues({
+        features,
+        persistedFeatureValues: {
+          fast_mode: true,
+          unknown_feature: true,
+        },
+        localFeatureValues: {},
+      }),
+    ).toEqual({
+      fast_mode: true,
+    });
+  });
+
+  it("prefers local values over persisted values", () => {
+    expect(
+      resolveFeatureValues({
+        features,
+        persistedFeatureValues: {
+          fast_mode: true,
+          plan_mode: false,
+        },
+        localFeatureValues: {
+          fast_mode: false,
+        },
+      }),
+    ).toEqual({
+      fast_mode: false,
+      plan_mode: false,
+    });
+  });
+});
diff --git a/packages/app/src/hooks/feature-preferences.ts b/packages/app/src/hooks/feature-preferences.ts
new file mode 100644
index 000000000..8fc3f1aaf
--- /dev/null
+++ b/packages/app/src/hooks/feature-preferences.ts
@@ -0,0 +1,60 @@
+import type { AgentFeature } from "@server/server/agent/agent-sdk-types";
+
+export function pruneFeatureValues(
+  featureValues: Record<string, unknown>,
+  features: AgentFeature[],
+): Record<string, unknown> {
+  const allowedFeatureIds = new Set(features.map((feature) => feature.id));
+  let changed = false;
+  const next: Record<string, unknown> = {};
+
+  for (const [featureId, value] of Object.entries(featureValues)) {
+    if (!allowedFeatureIds.has(featureId)) {
+      changed = true;
+      continue;
+    }
+    next[featureId] = value;
+  }
+
+  return changed ? next : featureValues;
+}
+
+export function applyFeatureValues(
+  features: AgentFeature[],
+  featureValues: Record<string, unknown>,
+): AgentFeature[] {
+  if (Object.keys(featureValues).length === 0) {
+    return features;
+  }
+
+  return features.map((feature) => {
+    if (!Object.prototype.hasOwnProperty.call(featureValues, feature.id)) {
+      return feature;
+    }
+
+    return {
+      ...feature,
+      value: featureValues[feature.id],
+    } as AgentFeature;
+  });
+}
+
+export function resolveFeatureValues(args: {
+  features: AgentFeature[];
+  persistedFeatureValues: Record<string, unknown>;
+  localFeatureValues: Record<string, unknown>;
+}): Record<string, unknown> {
+  const next: Record<string, unknown> = {};
+
+  for (const feature of args.features) {
+    if (Object.prototype.hasOwnProperty.call(args.localFeatureValues, feature.id)) {
+      next[feature.id] = args.localFeatureValues[feature.id];
+      continue;
+    }
+    if (Object.prototype.hasOwnProperty.call(args.persistedFeatureValues, feature.id)) {
+      next[feature.id] = args.persistedFeatureValues[feature.id];
+    }
+  }
+
+  return next;
+}
diff --git a/packages/app/src/hooks/use-agent-form-state.ts b/packages/app/src/hooks/use-agent-form-state.ts
index 09e0ae2fd..fcf939101 100644
--- a/packages/app/src/hooks/use-agent-form-state.ts
+++ b/packages/app/src/hooks/use-agent-form-state.ts
@@ -651,30 +651,29 @@ export function useAgentFormState(options: UseAgentFormStateOptions = {}): UseAg
   const persistFormPreferences = useCallback(async () => {
     const resolvedModel = resolveEffectiveModel(availableModels, formState.model);
     const modelId = resolvedModel?.id ?? formState.model;
-    const nextPreferences = mergeProviderPreferences({
-      preferences: preferences ?? {},
-      provider: formState.provider,
-      updates: {
-        model: modelId || undefined,
-        mode: formState.modeId || undefined,
-        ...(modelId && formState.thinkingOptionId
-          ? {
-              thinkingByModel: {
-                [modelId]: formState.thinkingOptionId,
-              },
-            }
-          : {}),
-      } satisfies Partial<ProviderPreferences>,
-    });
-
-    await updatePreferences(nextPreferences);
+    await updatePreferences((current) =>
+      mergeProviderPreferences({
+        preferences: current,
+        provider: formState.provider,
+        updates: {
+          model: modelId || undefined,
+          mode: formState.modeId || undefined,
+          ...(modelId && formState.thinkingOptionId
+            ? {
+                thinkingByModel: {
+                  [modelId]: formState.thinkingOptionId,
+                },
+              }
+            : {}),
+        } satisfies Partial<ProviderPreferences>,
+      }),
+    );
   }, [
     availableModels,
     formState.model,
     formState.modeId,
     formState.provider,
     formState.thinkingOptionId,
-    preferences?.providerPreferences,
     updatePreferences,
   ]);
 
diff --git a/packages/app/src/hooks/use-draft-agent-features.ts b/packages/app/src/hooks/use-draft-agent-features.ts
index eaef93d6f..3f9a4dce4 100644
--- a/packages/app/src/hooks/use-draft-agent-features.ts
+++ b/packages/app/src/hooks/use-draft-agent-features.ts
@@ -1,50 +1,16 @@
 import { useCallback, useEffect, useMemo, useState } from "react";
 import { useQuery } from "@tanstack/react-query";
 import type {
-  AgentFeature,
   AgentProvider,
   AgentSessionConfig,
 } from "@server/server/agent/agent-sdk-types";
 import { useHostRuntimeClient, useHostRuntimeIsConnected } from "@/runtime/host-runtime";
-
-function pruneFeatureValues(
-  featureValues: Record<string, unknown>,
-  features: AgentFeature[],
-): Record<string, unknown> {
-  const allowedFeatureIds = new Set(features.map((feature) => feature.id));
-  let changed = false;
-  const next: Record<string, unknown> = {};
-
-  for (const [featureId, value] of Object.entries(featureValues)) {
-    if (!allowedFeatureIds.has(featureId)) {
-      changed = true;
-      continue;
-    }
-    next[featureId] = value;
-  }
-
-  return changed ? next : featureValues;
-}
-
-function applyFeatureValues(
-  features: AgentFeature[],
-  featureValues: Record<string, unknown>,
-): AgentFeature[] {
-  if (Object.keys(featureValues).length === 0) {
-    return features;
-  }
-
-  return features.map((feature) => {
-    if (!Object.prototype.hasOwnProperty.call(featureValues, feature.id)) {
-      return feature;
-    }
-
-    return {
-      ...feature,
-      value: featureValues[feature.id],
-    } as AgentFeature;
-  });
-}
+import { mergeProviderPreferences, useFormPreferences } from "./use-form-preferences";
+import {
+  applyFeatureValues,
+  pruneFeatureValues,
+  resolveFeatureValues,
+} from "./feature-preferences";
 
 type DraftFeatureConfig = Pick<
   AgentSessionConfig,
@@ -60,10 +26,15 @@ export function useDraftAgentFeatures(input: {
   thinkingOptionId: string | null | undefined;
 }) {
   const { serverId, provider, cwd, modeId, modelId, thinkingOptionId } = input;
-  const [featureValues, setFeatureValues] = useState<Record<string, unknown>>({});
+  const [localFeatureValues, setLocalFeatureValues] = useState<Record<string, unknown>>({});
   const client = useHostRuntimeClient(serverId ?? "");
   const isConnected = useHostRuntimeIsConnected(serverId ?? "");
+  const { preferences, updatePreferences } = useFormPreferences();
   const normalizedCwd = cwd?.trim() || "";
+  const persistedFeatureValues = useMemo(
+    () => preferences.providerPreferences?.[provider]?.featureValues ?? {},
+    [preferences.providerPreferences, provider],
+  );
 
   const draftConfig = useMemo<DraftFeatureConfig | null>(() => {
     if (!normalizedCwd) {
@@ -102,28 +73,56 @@ export function useDraftAgentFeatures(input: {
       return payload.features ?? [];
     },
   });
+  const availableFeatures = featuresQuery.data ?? [];
+  const featureValues = useMemo(
+    () =>
+      resolveFeatureValues({
+        features: availableFeatures,
+        persistedFeatureValues,
+        localFeatureValues,
+      }),
+    [availableFeatures, localFeatureValues, persistedFeatureValues],
+  );
 
   const features = useMemo(() => {
-    return applyFeatureValues(featuresQuery.data ?? [], featureValues);
-  }, [featureValues, featuresQuery.data]);
+    return applyFeatureValues(availableFeatures, featureValues);
+  }, [availableFeatures, featureValues]);
 
   useEffect(() => {
-    const next = pruneFeatureValues(featureValues, features);
-    if (next !== featureValues) {
-      setFeatureValues(next);
+    setLocalFeatureValues({});
+  }, [provider]);
+
+  useEffect(() => {
+    const next = pruneFeatureValues(localFeatureValues, availableFeatures);
+    if (next !== localFeatureValues) {
+      setLocalFeatureValues(next);
     }
-  }, [featureValues, features]);
+  }, [availableFeatures, localFeatureValues]);
 
   const effectiveFeatureValues = Object.keys(featureValues).length > 0 ? featureValues : undefined;
   const setFeatureValue = useCallback((featureId: string, value: unknown) => {
-    setFeatureValues((current) => {
+    setLocalFeatureValues((current) => {
       if (Object.is(current[featureId], value)) {
         return current;
       }
 
       return { ...current, [featureId]: value };
     });
-  }, []);
+    void updatePreferences(
+      (current) =>
+        mergeProviderPreferences({
+          preferences: current,
+          provider,
+          updates: {
+            featureValues: {
+              [featureId]: value,
+            },
+          },
+        }),
+    ).catch((error) => {
+      console.warn("[useDraftAgentFeatures] persist feature preference failed", error);
+    });
+  }, [provider, updatePreferences]);
 
   return {
     features,
diff --git a/packages/app/src/hooks/use-form-preferences.test.ts b/packages/app/src/hooks/use-form-preferences.test.ts
index 55bb8fc56..4dd277420 100644
--- a/packages/app/src/hooks/use-form-preferences.test.ts
+++ b/packages/app/src/hooks/use-form-preferences.test.ts
@@ -59,6 +59,41 @@ describe("mergeProviderPreferences", () => {
       },
     });
   });
+
+  it("merges feature values without dropping existing entries", () => {
+    expect(
+      mergeProviderPreferences({
+        preferences: {
+          provider: "codex",
+          providerPreferences: {
+            codex: {
+              model: "gpt-5.4",
+              featureValues: {
+                fast_mode: true,
+              },
+            },
+          },
+        },
+        provider: "codex",
+        updates: {
+          featureValues: {
+            plan_mode: true,
+          },
+        },
+      }),
+    ).toEqual({
+      provider: "codex",
+      providerPreferences: {
+        codex: {
+          model: "gpt-5.4",
+          featureValues: {
+            fast_mode: true,
+            plan_mode: true,
+          },
+        },
+      },
+    });
+  });
 });
 
 describe("favorite model preferences", () => {
diff --git a/packages/app/src/hooks/use-form-preferences.ts b/packages/app/src/hooks/use-form-preferences.ts
index ff04c8e84..cd14ebf66 100644
--- a/packages/app/src/hooks/use-form-preferences.ts
+++ b/packages/app/src/hooks/use-form-preferences.ts
@@ -25,6 +25,7 @@ const providerPreferencesSchema = z.object({
   model: z.string().optional(),
   mode: z.string().optional(),
   thinkingByModel: z.record(z.string()).optional(),
+  featureValues: z.record(z.unknown()).optional(),
 });
 
 const formPreferencesSchema = z.object({
@@ -53,7 +54,9 @@ async function loadFormPreferences(): Promise<FormPreferences> {
 export interface UseFormPreferencesReturn {
   preferences: FormPreferences;
   isLoading: boolean;
-  updatePreferences: (updates: Partial<FormPreferences>) => Promise<void>;
+  updatePreferences: (
+    updates: Partial<FormPreferences> | ((current: FormPreferences) => FormPreferences),
+  ) => Promise<void>;
 }
 
 export function mergeProviderPreferences(args: {
@@ -71,6 +74,13 @@ export function mergeProviderPreferences(args: {
           ...existing.thinkingByModel,
           ...updates.thinkingByModel,
         };
+  const nextFeatureValues =
+    updates.featureValues === undefined
+      ? existing.featureValues
+      : {
+          ...existing.featureValues,
+          ...updates.featureValues,
+        };
 
   return {
     ...preferences,
@@ -81,6 +91,7 @@ export function mergeProviderPreferences(args: {
         ...existing,
         ...updates,
         ...(nextThinkingByModel ? { thinkingByModel: nextThinkingByModel } : {}),
+        ...(nextFeatureValues ? { featureValues: nextFeatureValues } : {}),
       },
     },
   };
@@ -133,11 +144,12 @@ export function useFormPreferences(): UseFormPreferencesReturn {
   const preferences = data ?? DEFAULT_FORM_PREFERENCES;
 
   const updatePreferences = useCallback(
-    async (updates: Partial<FormPreferences>) => {
+    async (updates: Partial<FormPreferences> | ((current: FormPreferences) => FormPreferences)) => {
       const prev =
         queryClient.getQueryData<FormPreferences>(FORM_PREFERENCES_QUERY_KEY) ??
         DEFAULT_FORM_PREFERENCES;
-      const next = { ...prev, ...updates };
+      const next =
+        typeof updates === "function" ? updates(prev) : { ...prev, ...updates };
       queryClient.setQueryData<FormPreferences>(FORM_PREFERENCES_QUERY_KEY, next);
       await AsyncStorage.setItem(FORM_PREFERENCES_STORAGE_KEY, JSON.stringify(next));
     },