diff --git a/esphome/core/application.cpp b/esphome/core/application.cpp
index cd75859880..0c17c70161 100644
--- a/esphome/core/application.cpp
+++ b/esphome/core/application.cpp
@@ -85,8 +85,12 @@ void Application::setup() {
     if (component->can_proceed())
       continue;
 
+    // Force the status LED to blink WARNING while we wait for a slow
+    // component to come up. Cleared after setup() finishes if no real
+    // component has warning set.
+    this->app_state_ |= STATUS_LED_WARNING;
+
     do {
-      uint8_t new_app_state = STATUS_LED_WARNING;
       uint32_t now = millis();
 
       // Process pending loop enables to handle GPIO interrupts during setup
@@ -96,17 +100,26 @@ void Application::setup() {
         // Update loop_component_start_time_ right before calling each component
         this->loop_component_start_time_ = millis();
         this->components_[j]->call();
-        new_app_state |= this->components_[j]->get_component_state();
-        this->app_state_ |= new_app_state;
         this->feed_wdt();
       }
 
       this->after_loop_tasks_();
-      this->app_state_ = new_app_state;
       yield();
     } while (!component->can_proceed() && !component->is_failed());
   }
 
+  // Setup is complete. Reconcile STATUS_LED_WARNING: the slow-setup path
+  // above may have forced it on, and any status_clear_warning() calls
+  // from components during setup were intentional no-ops (gated by
+  // APP_STATE_SETUP_COMPLETE). Walk components once here to pick up the
+  // real state. STATUS_LED_ERROR is never artificially forced, so its
+  // clear path always works and needs no reconciliation. Finally, set
+  // APP_STATE_SETUP_COMPLETE so subsequent warning clears go through
+  // the normal walk-and-clear path.
+  if (!this->any_component_has_status_flag_(STATUS_LED_WARNING))
+    this->app_state_ &= ~STATUS_LED_WARNING;
+  this->app_state_ |= APP_STATE_SETUP_COMPLETE;
+
   ESP_LOGI(TAG, "setup() finished successfully!");
 
 #ifdef USE_SETUP_PRIORITY_OVERRIDE
@@ -211,6 +224,19 @@ void HOT Application::feed_wdt(uint32_t time) {
 #endif
   }
 }
+bool Application::any_component_has_status_flag_(uint8_t flag) const {
+  // Walk all components (not just looping ones) so non-looping components'
+  // status bits are respected. Only called from the slow-path clear helpers
+  // (status_clear_warning_slow_path_ / status_clear_error_slow_path_) on an
+  // actual set→clear transition, so walking O(N) here is paid once per
+  // transition — not once per loop iteration.
+  for (auto *component : this->components_) {
+    if ((component->get_component_state() & flag) != 0)
+      return true;
+  }
+  return false;
+}
+
 void Application::reboot() {
   ESP_LOGI(TAG, "Forcing a reboot");
   for (auto &component : std::ranges::reverse_view(this->components_)) {
diff --git a/esphome/core/application.h b/esphome/core/application.h
index 6b2969b490..1a36058deb 100644
--- a/esphome/core/application.h
+++ b/esphome/core/application.h
@@ -401,7 +401,24 @@ class Application {
    */
   void teardown_components(uint32_t timeout_ms);
 
-  uint8_t get_app_state() const { return this->app_state_; }
+  /// Return the public app state bits (STATUS_LED_* and lifecycle).
+  /// Internal bookkeeping bits like APP_STATE_SETUP_COMPLETE are masked
+  /// out so external readers (status_led components, etc.) never see them.
+  uint8_t get_app_state() const { return this->app_state_ & ~APP_STATE_SETUP_COMPLETE; }
+
+  /// True once Application::setup() has finished walking all components
+  /// and finalized the initial status flags. Before this point, the
+  /// slow-setup busy-wait may be forcing STATUS_LED_WARNING on, and
+  /// status_clear_* intentionally skips its walk-and-clear step so the
+  /// forced bit doesn't get wiped. Stored as a free bit on app_state_
+  /// (bit 6) to avoid costing additional RAM.
+  bool is_setup_complete() const { return (this->app_state_ & APP_STATE_SETUP_COMPLETE) != 0; }
+
+  /// Walk all registered components looking for any whose component_state_
+  /// has the given flag set. Used by Component::status_clear_*_slow_path_()
+  /// to decide whether to clear the corresponding bit on this->app_state_
+  /// (which is the app-wide "any component has this status" indicator).
+  bool any_component_has_status_flag_(uint8_t flag) const;
 
 // Helper macro for entity getter method declarations
 #ifdef USE_DEVICES
@@ -838,8 +855,6 @@ inline void ESPHOME_ALWAYS_INLINE Application::before_loop_tasks_(uint32_t loop_
 }
 
 inline void ESPHOME_ALWAYS_INLINE Application::loop() {
-  uint8_t new_app_state = 0;
-
   // Get the initial loop time at the start
   uint32_t last_op_end_time = millis();
 
@@ -859,13 +874,10 @@ inline void ESPHOME_ALWAYS_INLINE Application::loop() {
       // Use the finish method to get the current time as the end time
       last_op_end_time = guard.finish();
     }
-    new_app_state |= component->get_component_state();
-    this->app_state_ |= new_app_state;
     this->feed_wdt(last_op_end_time);
   }
 
   this->after_loop_tasks_();
-  this->app_state_ = new_app_state;
 
 #ifdef USE_RUNTIME_STATS
   // Process any pending runtime stats printing after all components have run
diff --git a/esphome/core/component.cpp b/esphome/core/component.cpp
index deda42b0a7..8949b4b76d 100644
--- a/esphome/core/component.cpp
+++ b/esphome/core/component.cpp
@@ -411,10 +411,23 @@ void Component::status_set_error(const LogString *message) {
 }
 void Component::status_clear_warning_slow_path_() {
   this->component_state_ &= ~STATUS_LED_WARNING;
+  // Clear the app-wide STATUS_LED_WARNING bit only if setup has finished
+  // AND no other component still has it set. During setup the forced
+  // STATUS_LED_WARNING (from the slow-setup busy-wait) must not be wiped
+  // by a transient component clear — Application::setup() reconciles
+  // the warning bit once at the end before setting APP_STATE_SETUP_COMPLETE.
+  // The set path is unchanged (set_status_flag_ still writes directly).
+  if (App.is_setup_complete() && !App.any_component_has_status_flag_(STATUS_LED_WARNING))
+    App.app_state_ &= ~STATUS_LED_WARNING;
   ESP_LOGW(TAG, "%s cleared Warning flag", LOG_STR_ARG(this->get_component_log_str()));
 }
 void Component::status_clear_error_slow_path_() {
   this->component_state_ &= ~STATUS_LED_ERROR;
+  // STATUS_LED_ERROR is never artificially forced — it only ever lands
+  // in app_state_ via a real set_status_flag_ call. So the walk-and-clear
+  // path is always safe, including during setup.
+  if (!App.any_component_has_status_flag_(STATUS_LED_ERROR))
+    App.app_state_ &= ~STATUS_LED_ERROR;
   ESP_LOGE(TAG, "%s cleared Error flag", LOG_STR_ARG(this->get_component_log_str()));
 }
 void Component::status_momentary_warning(const char *name, uint32_t length) {
diff --git a/esphome/core/component.h b/esphome/core/component.h
index e2b7aa85d3..3307c5ae76 100644
--- a/esphome/core/component.h
+++ b/esphome/core/component.h
@@ -89,6 +89,11 @@ inline constexpr uint8_t STATUS_LED_WARNING = 0x08;
 inline constexpr uint8_t STATUS_LED_ERROR = 0x10;
 // Component loop override flag uses bit 5 (set at registration time)
 inline constexpr uint8_t COMPONENT_HAS_LOOP = 0x20;
+// Bit 6 on Application::app_state_ (ONLY) — set at the end of
+// Application::setup(). Component::status_clear_*_slow_path_() uses this to
+// decide whether to propagate clears to App.app_state_. Never set on a
+// Component's component_state_.
+inline constexpr uint8_t APP_STATE_SETUP_COMPLETE = 0x40;
 // Remove before 2026.8.0
 enum class RetryResult { DONE, RETRY };