diff --git a/auto-claude-ui/src/main/ipc-handlers/settings-handlers.ts b/auto-claude-ui/src/main/ipc-handlers/settings-handlers.ts
index 30f06a7d..25b1a763 100644
--- a/auto-claude-ui/src/main/ipc-handlers/settings-handlers.ts
+++ b/auto-claude-ui/src/main/ipc-handlers/settings-handlers.ts
@@ -94,7 +94,7 @@ export function registerSettingsHandlers(
   ipcMain.handle(
     IPC_CHANNELS.SETTINGS_GET,
     async (): Promise<IPCResult<AppSettings>> => {
-      let settings = { ...DEFAULT_APP_SETTINGS };
+      let settings: AppSettings = { ...DEFAULT_APP_SETTINGS };
       let needsSave = false;
 
       if (existsSync(settingsPath)) {
@@ -106,12 +106,15 @@ export function registerSettingsHandlers(
         }
       }
 
-      // Migration: Reset agent profile to 'auto' for existing users (one-time)
-      // This ensures all users get the optimized 'auto' profile as the default
-      const settingsAny = settings as Record<string, unknown>;
-      if (!settingsAny._migratedAgentProfileToAuto) {
-        settings.selectedAgentProfile = 'auto';
-        settingsAny._migratedAgentProfileToAuto = true;
+      // Migration: Set agent profile to 'auto' for users who haven't made a selection (one-time)
+      // This ensures new users get the optimized 'auto' profile as the default
+      // while preserving existing user preferences
+      if (!settings._migratedAgentProfileToAuto) {
+        // Only set 'auto' if user hasn't made a selection yet
+        if (!settings.selectedAgentProfile) {
+          settings.selectedAgentProfile = 'auto';
+        }
+        settings._migratedAgentProfileToAuto = true;
         needsSave = true;
       }
 
@@ -127,8 +130,9 @@ export function registerSettingsHandlers(
       if (needsSave) {
         try {
           writeFileSync(settingsPath, JSON.stringify(settings, null, 2));
-        } catch {
-          // Ignore write errors during migration
+        } catch (error) {
+          console.error('[SETTINGS_GET] Failed to persist migration:', error);
+          // Continue anyway - settings will be migrated in-memory for this session
         }
       }
 
diff --git a/auto-claude-ui/src/renderer/components/TaskCreationWizard.tsx b/auto-claude-ui/src/renderer/components/TaskCreationWizard.tsx
index 6aaa57d9..58b4c449 100644
--- a/auto-claude-ui/src/renderer/components/TaskCreationWizard.tsx
+++ b/auto-claude-ui/src/renderer/components/TaskCreationWizard.tsx
@@ -102,11 +102,12 @@ export function TaskCreationWizard({
   const [model, setModel] = useState<ModelType | ''>(selectedProfile.model);
   const [thinkingLevel, setThinkingLevel] = useState<ThinkingLevel | ''>(selectedProfile.thinkingLevel);
   // Auto profile - per-phase configuration
+  // Use custom settings from app settings if available, otherwise fall back to defaults
   const [phaseModels, setPhaseModels] = useState<PhaseModelConfig | undefined>(
-    selectedProfile.phaseModels || DEFAULT_PHASE_MODELS
+    settings.customPhaseModels || selectedProfile.phaseModels || DEFAULT_PHASE_MODELS
   );
   const [phaseThinking, setPhaseThinking] = useState<PhaseThinkingConfig | undefined>(
-    selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING
+    settings.customPhaseThinking || selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING
   );
 
   // Image attachments
@@ -143,8 +144,8 @@ export function TaskCreationWizard({
         setProfileId(draft.profileId || settings.selectedAgentProfile || 'auto');
         setModel(draft.model || selectedProfile.model);
         setThinkingLevel(draft.thinkingLevel || selectedProfile.thinkingLevel);
-        setPhaseModels(draft.phaseModels || selectedProfile.phaseModels || DEFAULT_PHASE_MODELS);
-        setPhaseThinking(draft.phaseThinking || selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING);
+        setPhaseModels(draft.phaseModels || settings.customPhaseModels || selectedProfile.phaseModels || DEFAULT_PHASE_MODELS);
+        setPhaseThinking(draft.phaseThinking || settings.customPhaseThinking || selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING);
         setImages(draft.images);
         setReferencedFiles(draft.referencedFiles ?? []);
         setRequireReviewBeforeCoding(draft.requireReviewBeforeCoding ?? false);
@@ -159,15 +160,15 @@ export function TaskCreationWizard({
         }
         // Note: Referenced Files section is always visible, no need to expand
       } else {
-        // No draft - initialize from selected profile
+        // No draft - initialize from selected profile and custom settings
         setProfileId(settings.selectedAgentProfile || 'auto');
         setModel(selectedProfile.model);
         setThinkingLevel(selectedProfile.thinkingLevel);
-        setPhaseModels(selectedProfile.phaseModels || DEFAULT_PHASE_MODELS);
-        setPhaseThinking(selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING);
+        setPhaseModels(settings.customPhaseModels || selectedProfile.phaseModels || DEFAULT_PHASE_MODELS);
+        setPhaseThinking(settings.customPhaseThinking || selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING);
       }
     }
-  }, [open, projectId, settings.selectedAgentProfile, selectedProfile.model, selectedProfile.thinkingLevel]);
+  }, [open, projectId, settings.selectedAgentProfile, settings.customPhaseModels, settings.customPhaseThinking, selectedProfile.model, selectedProfile.thinkingLevel]);
 
   // Fetch branches and project default branch when dialog opens
   useEffect(() => {
@@ -542,12 +543,12 @@ export function TaskCreationWizard({
     setPriority('');
     setComplexity('');
     setImpact('');
-    // Reset to selected profile defaults
+    // Reset to selected profile defaults and custom settings
     setProfileId(settings.selectedAgentProfile || 'auto');
     setModel(selectedProfile.model);
     setThinkingLevel(selectedProfile.thinkingLevel);
-    setPhaseModels(selectedProfile.phaseModels || DEFAULT_PHASE_MODELS);
-    setPhaseThinking(selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING);
+    setPhaseModels(settings.customPhaseModels || selectedProfile.phaseModels || DEFAULT_PHASE_MODELS);
+    setPhaseThinking(settings.customPhaseThinking || selectedProfile.phaseThinking || DEFAULT_PHASE_THINKING);
     setImages([]);
     setReferencedFiles([]);
     setRequireReviewBeforeCoding(false);
diff --git a/auto-claude-ui/src/renderer/components/settings/AgentProfileSettings.tsx b/auto-claude-ui/src/renderer/components/settings/AgentProfileSettings.tsx
index eb119815..08a51f32 100644
--- a/auto-claude-ui/src/renderer/components/settings/AgentProfileSettings.tsx
+++ b/auto-claude-ui/src/renderer/components/settings/AgentProfileSettings.tsx
@@ -1,9 +1,25 @@
-import { Brain, Scale, Zap, Check, Sparkles } from 'lucide-react';
+import { useState } from 'react';
+import { Brain, Scale, Zap, Check, Sparkles, ChevronDown, ChevronUp, RotateCcw } from 'lucide-react';
 import { cn } from '../../lib/utils';
-import { DEFAULT_AGENT_PROFILES, AVAILABLE_MODELS, THINKING_LEVELS } from '../../../shared/constants';
+import {
+  DEFAULT_AGENT_PROFILES,
+  AVAILABLE_MODELS,
+  THINKING_LEVELS,
+  DEFAULT_PHASE_MODELS,
+  DEFAULT_PHASE_THINKING
+} from '../../../shared/constants';
 import { useSettingsStore, saveSettings } from '../../stores/settings-store';
 import { SettingsSection } from './SettingsSection';
-import type { AgentProfile } from '../../../shared/types/settings';
+import { Label } from '../ui/label';
+import { Button } from '../ui/button';
+import {
+  Select,
+  SelectContent,
+  SelectItem,
+  SelectTrigger,
+  SelectValue
+} from '../ui/select';
+import type { AgentProfile, PhaseModelConfig, PhaseThinkingConfig, ModelTypeShort, ThinkingLevel } from '../../../shared/types/settings';
 
 /**
  * Icon mapping for agent profile icons
@@ -15,6 +31,13 @@ const iconMap: Record<string, React.ElementType> = {
   Sparkles
 };
 
+const PHASE_LABELS: Record<keyof PhaseModelConfig, { label: string; description: string }> = {
+  spec: { label: 'Spec Creation', description: 'Discovery, requirements, context gathering' },
+  planning: { label: 'Planning', description: 'Implementation planning and architecture' },
+  coding: { label: 'Coding', description: 'Actual code implementation' },
+  qa: { label: 'QA Review', description: 'Quality assurance and validation' }
+};
+
 /**
  * Agent Profile Settings component
  * Displays preset agent profiles for quick model/thinking level configuration
@@ -23,9 +46,40 @@ const iconMap: Record<string, React.ElementType> = {
 export function AgentProfileSettings() {
   const settings = useSettingsStore((state) => state.settings);
   const selectedProfileId = settings.selectedAgentProfile || 'auto';
+  const [showPhaseConfig, setShowPhaseConfig] = useState(selectedProfileId === 'auto');
+
+  // Get current phase config from settings or defaults
+  const currentPhaseModels: PhaseModelConfig = settings.customPhaseModels || DEFAULT_PHASE_MODELS;
+  const currentPhaseThinking: PhaseThinkingConfig = settings.customPhaseThinking || DEFAULT_PHASE_THINKING;
 
   const handleSelectProfile = async (profileId: string) => {
-    await saveSettings({ selectedAgentProfile: profileId });
+    const success = await saveSettings({ selectedAgentProfile: profileId });
+    if (!success) {
+      // Log error for debugging - in future could show user toast notification
+      console.error('Failed to save agent profile selection');
+      return;
+    }
+    // Auto-expand phase config when Auto profile is selected
+    if (profileId === 'auto') {
+      setShowPhaseConfig(true);
+    }
+  };
+
+  const handlePhaseModelChange = async (phase: keyof PhaseModelConfig, value: ModelTypeShort) => {
+    const newPhaseModels = { ...currentPhaseModels, [phase]: value };
+    await saveSettings({ customPhaseModels: newPhaseModels });
+  };
+
+  const handlePhaseThinkingChange = async (phase: keyof PhaseThinkingConfig, value: ThinkingLevel) => {
+    const newPhaseThinking = { ...currentPhaseThinking, [phase]: value };
+    await saveSettings({ customPhaseThinking: newPhaseThinking });
+  };
+
+  const handleResetToDefaults = async () => {
+    await saveSettings({
+      customPhaseModels: DEFAULT_PHASE_MODELS,
+      customPhaseThinking: DEFAULT_PHASE_THINKING
+    });
   };
 
   /**
@@ -44,6 +98,18 @@ export function AgentProfileSettings() {
     return level?.label || thinkingValue;
   };
 
+  /**
+   * Check if current config differs from defaults
+   */
+  const hasCustomConfig = (): boolean => {
+    const phases: Array<keyof PhaseModelConfig> = ['spec', 'planning', 'coding', 'qa'];
+    return phases.some(
+      phase =>
+        currentPhaseModels[phase] !== DEFAULT_PHASE_MODELS[phase] ||
+        currentPhaseThinking[phase] !== DEFAULT_PHASE_THINKING[phase]
+    );
+  };
+
   /**
    * Render a single profile card
    */
@@ -126,6 +192,112 @@ export function AgentProfileSettings() {
         <div className="grid grid-cols-1 lg:grid-cols-2 gap-3">
           {DEFAULT_AGENT_PROFILES.map(renderProfileCard)}
         </div>
+
+        {/* Phase Configuration (only for Auto profile) */}
+        {selectedProfileId === 'auto' && (
+          <div className="mt-6 rounded-lg border border-border bg-card">
+            {/* Header - Collapsible */}
+            <button
+              type="button"
+              onClick={() => setShowPhaseConfig(!showPhaseConfig)}
+              className="flex w-full items-center justify-between p-4 text-left hover:bg-muted/50 transition-colors rounded-t-lg"
+            >
+              <div>
+                <h4 className="font-medium text-sm text-foreground">Phase Configuration</h4>
+                <p className="text-xs text-muted-foreground mt-0.5">
+                  Customize model and thinking level for each phase
+                </p>
+              </div>
+              {showPhaseConfig ? (
+                <ChevronUp className="h-4 w-4 text-muted-foreground" />
+              ) : (
+                <ChevronDown className="h-4 w-4 text-muted-foreground" />
+              )}
+            </button>
+
+            {/* Phase Configuration Content */}
+            {showPhaseConfig && (
+              <div className="border-t border-border p-4 space-y-4">
+                {/* Reset button */}
+                {hasCustomConfig() && (
+                  <div className="flex justify-end">
+                    <Button
+                      variant="ghost"
+                      size="sm"
+                      onClick={handleResetToDefaults}
+                      className="text-xs h-7"
+                    >
+                      <RotateCcw className="h-3 w-3 mr-1.5" />
+                      Reset to defaults
+                    </Button>
+                  </div>
+                )}
+
+                {/* Phase Configuration Grid */}
+                <div className="space-y-4">
+                  {(Object.keys(PHASE_LABELS) as Array<keyof PhaseModelConfig>).map((phase) => (
+                    <div key={phase} className="space-y-2">
+                      <div className="flex items-center justify-between">
+                        <Label className="text-sm font-medium text-foreground">
+                          {PHASE_LABELS[phase].label}
+                        </Label>
+                        <span className="text-xs text-muted-foreground">
+                          {PHASE_LABELS[phase].description}
+                        </span>
+                      </div>
+                      <div className="grid grid-cols-2 gap-3">
+                        {/* Model Select */}
+                        <div className="space-y-1">
+                          <Label className="text-xs text-muted-foreground">Model</Label>
+                          <Select
+                            value={currentPhaseModels[phase]}
+                            onValueChange={(value) => handlePhaseModelChange(phase, value as ModelTypeShort)}
+                          >
+                            <SelectTrigger className="h-9">
+                              <SelectValue />
+                            </SelectTrigger>
+                            <SelectContent>
+                              {AVAILABLE_MODELS.map((m) => (
+                                <SelectItem key={m.value} value={m.value}>
+                                  {m.label}
+                                </SelectItem>
+                              ))}
+                            </SelectContent>
+                          </Select>
+                        </div>
+                        {/* Thinking Level Select */}
+                        <div className="space-y-1">
+                          <Label className="text-xs text-muted-foreground">Thinking Level</Label>
+                          <Select
+                            value={currentPhaseThinking[phase]}
+                            onValueChange={(value) => handlePhaseThinkingChange(phase, value as ThinkingLevel)}
+                          >
+                            <SelectTrigger className="h-9">
+                              <SelectValue />
+                            </SelectTrigger>
+                            <SelectContent>
+                              {THINKING_LEVELS.map((level) => (
+                                <SelectItem key={level.value} value={level.value}>
+                                  {level.label}
+                                </SelectItem>
+                              ))}
+                            </SelectContent>
+                          </Select>
+                        </div>
+                      </div>
+                    </div>
+                  ))}
+                </div>
+
+                {/* Info note */}
+                <p className="text-[10px] text-muted-foreground mt-4 pt-3 border-t border-border">
+                  These settings will be used as defaults when creating new tasks with the Auto profile.
+                  You can override them per-task in the task creation wizard.
+                </p>
+              </div>
+            )}
+          </div>
+        )}
       </div>
     </SettingsSection>
   );
diff --git a/auto-claude-ui/src/shared/types/settings.ts b/auto-claude-ui/src/shared/types/settings.ts
index 0ff41b41..2f06f569 100644
--- a/auto-claude-ui/src/shared/types/settings.ts
+++ b/auto-claude-ui/src/shared/types/settings.ts
@@ -82,10 +82,15 @@ export interface AppSettings {
   onboardingCompleted?: boolean;
   // Selected agent profile for preset model/thinking configurations
   selectedAgentProfile?: string;
+  // Custom phase configuration for Auto profile (overrides defaults)
+  customPhaseModels?: PhaseModelConfig;
+  customPhaseThinking?: PhaseThinkingConfig;
   // Changelog preferences
   changelogFormat?: ChangelogFormat;
   changelogAudience?: ChangelogAudience;
   changelogEmojiLevel?: ChangelogEmojiLevel;
+  // Migration flags (internal use)
+  _migratedAgentProfileToAuto?: boolean;
 }
 
 // Auto-Claude Source Environment Configuration (for auto-claude repo .env)