diff --git a/esphome/core/application.h b/esphome/core/application.h
index 4a18714d0d..5baf570e62 100644
--- a/esphome/core/application.h
+++ b/esphome/core/application.h
@@ -637,10 +637,12 @@ inline void ESPHOME_ALWAYS_INLINE Application::loop() {
   // flag preserves it. wake_request_take() exchange-clears the flag; wakes
   // that arrive during Phase B re-set it and run Phase B again on the next
   // iteration.
-  const bool high_frequency = HighFrequencyLoopRequester::is_high_frequency();
-  const uint32_t elapsed = now - this->last_loop_;
-  const bool woke = esphome::wake_request_take();
-  const bool do_component_phase = high_frequency || woke || (elapsed >= this->loop_interval_);
+  //
+  // wake_request_take() must always be called first since it does an
+  // atomic exchange to clear the flag, and we want to run the component phase
+  // if either the flag was set or the scheduler requested a high-frequency loop.
+  const bool do_component_phase = esphome::wake_request_take() || HighFrequencyLoopRequester::is_high_frequency() ||
+                                  (now - this->last_loop_ >= this->loop_interval_);
 
   if (do_component_phase) {
     ComponentPhaseGuard phase_guard{*this};