diff --git a/esphome/core/application.cpp b/esphome/core/application.cpp
index 748c8f2237..873f342277 100644
--- a/esphome/core/application.cpp
+++ b/esphome/core/application.cpp
@@ -71,8 +71,11 @@ void Application::setup() {
 
     do {
       uint8_t new_app_state = STATUS_LED_WARNING;
-      this->scheduler.call(millis());
-      this->feed_wdt();
+      uint32_t now = millis();
+
+      // Process pending loop enables to handle GPIO interrupts during setup
+      this->before_loop_tasks_(now);
+
       for (uint32_t j = 0; j <= i; j++) {
         // Update loop_component_start_time_ right before calling each component
         this->loop_component_start_time_ = millis();
@@ -81,6 +84,8 @@ void Application::setup() {
         this->app_state_ |= new_app_state;
         this->feed_wdt();
       }
+
+      this->after_loop_tasks_();
       this->app_state_ = new_app_state;
       yield();
     } while (!component->can_proceed());
@@ -100,27 +105,7 @@ void Application::loop() {
   // Get the initial loop time at the start
   uint32_t last_op_end_time = millis();
 
-  this->scheduler.call(last_op_end_time);
-
-  // Feed WDT with time
-  this->feed_wdt(last_op_end_time);
-
-  // Process any pending enable_loop requests from ISRs
-  // This must be done before marking in_loop_ = true to avoid race conditions
-  if (this->has_pending_enable_loop_requests_) {
-    // Clear flag BEFORE processing to avoid race condition
-    // If ISR sets it during processing, we'll catch it next loop iteration
-    // This is safe because:
-    // 1. Each component has its own pending_enable_loop_ flag that we check
-    // 2. If we can't process a component (wrong state), enable_pending_loops_()
-    //    will set this flag back to true
-    // 3. Any new ISR requests during processing will set the flag again
-    this->has_pending_enable_loop_requests_ = false;
-    this->enable_pending_loops_();
-  }
-
-  // Mark that we're in the loop for safe reentrant modifications
-  this->in_loop_ = true;
+  this->before_loop_tasks_(last_op_end_time);
 
   for (this->current_loop_index_ = 0; this->current_loop_index_ < this->looping_components_active_end_;
        this->current_loop_index_++) {
@@ -141,7 +126,7 @@ void Application::loop() {
     this->feed_wdt(last_op_end_time);
   }
 
-  this->in_loop_ = false;
+  this->after_loop_tasks_();
   this->app_state_ = new_app_state;
 
 #ifdef USE_RUNTIME_STATS
@@ -411,6 +396,36 @@ void Application::enable_pending_loops_() {
   }
 }
 
+void Application::before_loop_tasks_(uint32_t loop_start_time) {
+  // Process scheduled tasks
+  this->scheduler.call(loop_start_time);
+
+  // Feed the watchdog timer
+  this->feed_wdt(loop_start_time);
+
+  // Process any pending enable_loop requests from ISRs
+  // This must be done before marking in_loop_ = true to avoid race conditions
+  if (this->has_pending_enable_loop_requests_) {
+    // Clear flag BEFORE processing to avoid race condition
+    // If ISR sets it during processing, we'll catch it next loop iteration
+    // This is safe because:
+    // 1. Each component has its own pending_enable_loop_ flag that we check
+    // 2. If we can't process a component (wrong state), enable_pending_loops_()
+    //    will set this flag back to true
+    // 3. Any new ISR requests during processing will set the flag again
+    this->has_pending_enable_loop_requests_ = false;
+    this->enable_pending_loops_();
+  }
+
+  // Mark that we're in the loop for safe reentrant modifications
+  this->in_loop_ = true;
+}
+
+void Application::after_loop_tasks_() {
+  // Clear the in_loop_ flag to indicate we're done processing components
+  this->in_loop_ = false;
+}
+
 #ifdef USE_SOCKET_SELECT_SUPPORT
 bool Application::register_socket_fd(int fd) {
   // WARNING: This function is NOT thread-safe and must only be called from the main loop
diff --git a/esphome/core/application.h b/esphome/core/application.h
index 75b9769ca3..a83789837f 100644
--- a/esphome/core/application.h
+++ b/esphome/core/application.h
@@ -512,6 +512,8 @@ class Application {
   void enable_component_loop_(Component *component);
   void enable_pending_loops_();
   void activate_looping_component_(uint16_t index);
+  void before_loop_tasks_(uint32_t loop_start_time);
+  void after_loop_tasks_();
 
   void feed_wdt_arch_();