diff --git a/src/App.vue b/src/App.vue
index 070ab5c..7ae72d6 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { onMounted } from 'vue'
+import { onMounted, watch } from 'vue'
 import TitleBar from './components/TitleBar.vue'
 import NavRail from './components/NavRail.vue'
 import ToastNotification from './components/ToastNotification.vue'
@@ -7,6 +7,20 @@ import { useSettingsStore } from './stores/settings'
 
 const settingsStore = useSettingsStore()
 
+function applyTheme() {
+  const el = document.documentElement
+  const mode = settingsStore.settings.theme_mode || 'dark'
+  const accent = settingsStore.settings.accent_color || 'amber'
+
+  if (mode === 'system') {
+    const prefersDark = window.matchMedia('(prefers-color-scheme: dark)').matches
+    el.setAttribute('data-theme', prefersDark ? 'dark' : 'light')
+  } else {
+    el.setAttribute('data-theme', mode)
+  }
+  el.setAttribute('data-accent', accent)
+}
+
 onMounted(async () => {
   await settingsStore.fetchSettings()
   const zoom = parseInt(settingsStore.settings.ui_zoom) || 100
@@ -14,6 +28,15 @@ onMounted(async () => {
   if (app) {
     (app.style as any).zoom = `${zoom}%`
   }
+  applyTheme()
+
+  window.matchMedia('(prefers-color-scheme: dark)').addEventListener('change', () => {
+    if (settingsStore.settings.theme_mode === 'system') applyTheme()
+  })
+})
+
+watch(() => [settingsStore.settings.theme_mode, settingsStore.settings.accent_color], () => {
+  applyTheme()
 })
 </script>
 
diff --git a/src/styles/main.css b/src/styles/main.css
index 58141c0..7b08f65 100644
--- a/src/styles/main.css
+++ b/src/styles/main.css
@@ -34,6 +34,63 @@
   --font-mono: 'JetBrains Mono', 'IBM Plex Mono', monospace;
 }
 
+/* Accent color overrides */
+[data-accent="amber"] {
+  --color-accent: #D97706;
+  --color-accent-hover: #B45309;
+  --color-accent-muted: rgba(217, 119, 6, 0.12);
+  --color-accent-text: #FBBF24;
+}
+[data-accent="blue"] {
+  --color-accent: #3B82F6;
+  --color-accent-hover: #2563EB;
+  --color-accent-muted: rgba(59, 130, 246, 0.12);
+  --color-accent-text: #60A5FA;
+}
+[data-accent="purple"] {
+  --color-accent: #8B5CF6;
+  --color-accent-hover: #7C3AED;
+  --color-accent-muted: rgba(139, 92, 246, 0.12);
+  --color-accent-text: #A78BFA;
+}
+[data-accent="green"] {
+  --color-accent: #10B981;
+  --color-accent-hover: #059669;
+  --color-accent-muted: rgba(16, 185, 129, 0.12);
+  --color-accent-text: #34D399;
+}
+[data-accent="red"] {
+  --color-accent: #EF4444;
+  --color-accent-hover: #DC2626;
+  --color-accent-muted: rgba(239, 68, 68, 0.12);
+  --color-accent-text: #F87171;
+}
+[data-accent="pink"] {
+  --color-accent: #EC4899;
+  --color-accent-hover: #DB2777;
+  --color-accent-muted: rgba(236, 72, 153, 0.12);
+  --color-accent-text: #F472B6;
+}
+[data-accent="cyan"] {
+  --color-accent: #06B6D4;
+  --color-accent-hover: #0891B2;
+  --color-accent-muted: rgba(6, 182, 212, 0.12);
+  --color-accent-text: #22D3EE;
+}
+
+/* Light mode */
+[data-theme="light"] {
+  --color-bg-base: #FAFAF9;
+  --color-bg-surface: #FFFFFF;
+  --color-bg-elevated: #F5F5F4;
+  --color-bg-inset: #E7E5E4;
+  --color-text-primary: #1C1917;
+  --color-text-secondary: #57534E;
+  --color-text-tertiary: #A8A29E;
+  --color-border-subtle: #E7E5E4;
+  --color-border-visible: #D6D3D1;
+}
+
 @layer base {
   * {
     margin: 0;
@@ -173,3 +230,18 @@
 .animate-pulse-colon {
   animation: pulse-colon 1s ease-in-out infinite;
 }
+
+/* Markdown inline styles */
+.markdown-inline strong { font-weight: 600; }
+.markdown-inline em { font-style: italic; }
+.markdown-inline code {
+  padding: 0.1em 0.3em;
+  background: var(--color-bg-elevated);
+  border-radius: 3px;
+  font-family: var(--font-mono);
+  font-size: 0.85em;
+}
+.markdown-inline a {
+  color: var(--color-accent-text);
+  text-decoration: underline;
+}
diff --git a/src/views/Settings.vue b/src/views/Settings.vue
index d4fa3ba..779d706 100644
--- a/src/views/Settings.vue
+++ b/src/views/Settings.vue
@@ -91,6 +91,44 @@
             />
           </div>
         </div>
+
+        <div class="border-t border-border-subtle mt-5 pt-5">
+          <div class="flex items-center justify-between">
+            <div>
+              <p class="text-[0.8125rem] text-text-primary">Theme</p>
+              <p class="text-[0.6875rem] text-text-tertiary mt-0.5">Light or dark appearance</p>
+            </div>
+            <div class="w-40">
+              <AppSelect
+                v-model="themeMode"
+                :options="themeModes"
+                label-key="label"
+                value-key="value"
+                placeholder="Dark"
+                :placeholder-value="'dark'"
+                @update:model-value="saveThemeSettings"
+              />
+            </div>
+          </div>
+
+          <div class="flex items-center justify-between mt-5">
+            <div>
+              <p class="text-[0.8125rem] text-text-primary">Accent Color</p>
+              <p class="text-[0.6875rem] text-text-tertiary mt-0.5">Primary interface color</p>
+            </div>
+            <div class="flex gap-2">
+              <button
+                v-for="ac in accentColors"
+                :key="ac.value"
+                @click="accentColor = ac.value; saveThemeSettings()"
+                class="w-6 h-6 rounded-full border-2 transition-all hover:scale-110 cursor-pointer"
+                :class="accentColor === ac.value ? 'border-text-primary scale-110' : 'border-transparent'"
+                :style="{ backgroundColor: ac.color }"
+                :title="ac.label"
+              />
+            </div>
+          </div>
+        </div>
       </div>
 
       <!-- Timer -->
@@ -120,22 +158,76 @@
             </button>
           </div>
 
-          <!-- Reminder Interval — progressive disclosure -->
-          <div
-            v-if="idleDetection"
-            class="flex items-center justify-between pl-4 border-l-2 border-border-subtle ml-1"
-          >
-            <div>
-              <p class="text-[0.8125rem] text-text-primary">Reminder Interval</p>
-              <p class="text-[0.6875rem] text-text-tertiary mt-0.5">Minutes between reminders while running</p>
+          <!-- Idle sub-settings — progressive disclosure -->
+          <div v-if="idleDetection" class="space-y-5 pl-4 border-l-2 border-border-subtle ml-1">
+            <div class="flex items-center justify-between">
+              <div>
+                <p class="text-[0.8125rem] text-text-primary">Idle Timeout</p>
+                <p class="text-[0.6875rem] text-text-tertiary mt-0.5">Minutes before idle pause triggers</p>
+              </div>
+              <AppNumberInput
+                v-model="idleTimeout"
+                :min="1"
+                :max="60"
+                :step="1"
+                :precision="0"
+                suffix="min"
+                @update:model-value="saveSettings"
+              />
             </div>
-            <input
-              v-model.number="reminderInterval"
-              type="number"
-              min="0"
-              max="120"
-              class="w-20 px-3 py-1.5 bg-bg-inset border border-border-subtle rounded-lg text-[0.8125rem] text-text-primary text-right font-mono focus:outline-none focus:border-border-visible"
-              @change="saveSettings"
+            <div class="flex items-center justify-between">
+              <div>
+                <p class="text-[0.8125rem] text-text-primary">Reminder Interval</p>
+                <p class="text-[0.6875rem] text-text-tertiary mt-0.5">Minutes between reminders while running</p>
+              </div>
+              <AppNumberInput
+                v-model="reminderInterval"
+                :min="0"
+                :max="120"
+                :step="5"
+                :precision="0"
+                suffix="min"
+                @update:model-value="saveSettings"
+              />
+            </div>
+          </div>
+
+          <!-- Divider -->
+          <div class="border-t border-border-subtle" />
+
+          <!-- App Tracking Mode -->
+          <div class="flex items-center justify-between">
+            <div>
+              <p class="text-[0.8125rem] text-text-primary">App Tracking Mode</p>
+              <p class="text-[0.6875rem] text-text-tertiary mt-0.5">What happens when a tracked app leaves focus</p>
+            </div>
+            <div class="w-48">
+              <AppSelect
+                v-model="appTrackingMode"
+                :options="appTrackingModes"
+                label-key="label"
+                value-key="value"
+                placeholder="Auto-pause"
+                :placeholder-value="'auto'"
+                @update:model-value="saveSettings"
+              />
+            </div>
+          </div>
+
+          <!-- Check Interval -->
+          <div class="flex items-center justify-between">
+            <div>
+              <p class="text-[0.8125rem] text-text-primary">Check Interval</p>
+              <p class="text-[0.6875rem] text-text-tertiary mt-0.5">How often to check idle & app visibility</p>
+            </div>
+            <AppNumberInput
+              v-model="appCheckInterval"
+              :min="1"
+              :max="60"
+              :step="1"
+              :precision="0"
+              suffix="sec"
+              @update:model-value="saveSettings"
             />
           </div>
         </div>
@@ -259,11 +351,38 @@ const activeTab = ref('general')
 // Settings state
 const hourlyRate = ref(0)
 const idleDetection = ref(true)
+const idleTimeout = ref(5)
 const reminderInterval = ref(15)
+const appTrackingMode = ref('auto')
+const appCheckInterval = ref(5)
 const zoomLevel = ref(100)
 const locale = ref('system')
 const currency = ref('USD')
 const currencyOptions = getCurrencies()
+const themeMode = ref('dark')
+const accentColor = ref('amber')
+
+const themeModes = [
+  { value: 'dark', label: 'Dark' },
+  { value: 'light', label: 'Light' },
+  { value: 'system', label: 'System' },
+]
+
+const accentColors = [
+  { value: 'amber', label: 'Amber', color: '#D97706' },
+  { value: 'blue', label: 'Blue', color: '#3B82F6' },
+  { value: 'purple', label: 'Purple', color: '#8B5CF6' },
+  { value: 'green', label: 'Green', color: '#10B981' },
+  { value: 'red', label: 'Red', color: '#EF4444' },
+  { value: 'pink', label: 'Pink', color: '#EC4899' },
+  { value: 'cyan', label: 'Cyan', color: '#06B6D4' },
+]
+
+const appTrackingModes = [
+  { value: 'auto', label: 'Auto-pause/resume' },
+  { value: 'notify', label: 'Notify + auto-resume' },
+  { value: 'prompt', label: 'Prompt user' },
+]
 
 // Dialog state
 const showClearDataDialog = ref(false)
@@ -312,7 +431,10 @@ async function saveSettings() {
   try {
     await settingsStore.updateSetting('hourly_rate', hourlyRate.value.toString())
     await settingsStore.updateSetting('idle_detection', idleDetection.value.toString())
+    await settingsStore.updateSetting('idle_timeout', idleTimeout.value.toString())
     await settingsStore.updateSetting('reminder_interval', reminderInterval.value.toString())
+    await settingsStore.updateSetting('app_tracking_mode', appTrackingMode.value)
+    await settingsStore.updateSetting('app_check_interval', appCheckInterval.value.toString())
   } catch (error) {
     console.error('Failed to save settings:', error)
     toastStore.error('Failed to save settings')
@@ -325,6 +447,12 @@ async function saveLocaleSettings() {
   await settingsStore.updateSetting('currency', currency.value)
 }
 
+// Save theme settings
+async function saveThemeSettings() {
+  await settingsStore.updateSetting('theme_mode', themeMode.value)
+  await settingsStore.updateSetting('accent_color', accentColor.value)
+}
+
 // Export all data
 async function exportData() {
   try {
@@ -362,9 +490,14 @@ onMounted(async () => {
 
   hourlyRate.value = parseFloat(settingsStore.settings.hourly_rate) || 0
   idleDetection.value = settingsStore.settings.idle_detection !== 'false'
+  idleTimeout.value = parseInt(settingsStore.settings.idle_timeout) || 5
   reminderInterval.value = parseInt(settingsStore.settings.reminder_interval) || 15
+  appTrackingMode.value = settingsStore.settings.app_tracking_mode || 'auto'
+  appCheckInterval.value = parseInt(settingsStore.settings.app_check_interval) || 5
   zoomLevel.value = parseInt(settingsStore.settings.ui_zoom) || 100
   locale.value = settingsStore.settings.locale || 'system'
   currency.value = settingsStore.settings.currency || 'USD'
+  themeMode.value = settingsStore.settings.theme_mode || 'dark'
+  accentColor.value = settingsStore.settings.accent_color || 'amber'
 })
 </script>