diff --git a/esphome/core/application.cpp b/esphome/core/application.cpp
index 606bcb9eb1..a36a236ee7 100644
--- a/esphome/core/application.cpp
+++ b/esphome/core/application.cpp
@@ -78,7 +78,7 @@ void Application::setup() {
     Component *component = this->components_[i];
 
     // Update loop_component_start_time_ before calling each component during setup
-    this->loop_component_start_time_ = millis();
+    this->loop_component_start_time_ = MillisInternal::get();
     component->call();
     this->scheduler.process_to_add();
     this->feed_wdt();
@@ -91,14 +91,14 @@ void Application::setup() {
     this->app_state_ |= STATUS_LED_WARNING;
 
     do {
-      uint32_t now = millis();
+      uint32_t now = MillisInternal::get();
 
       // 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();
+        this->loop_component_start_time_ = MillisInternal::get();
         this->components_[j]->call();
         this->feed_wdt();
       }
@@ -212,7 +212,7 @@ void Application::process_dump_config_() {
 void Application::feed_wdt() {
   // Cold entry: callers without a millis() timestamp in hand. Fetches the
   // time and takes the same rate-limit path as feed_wdt_with_time().
-  uint32_t now = millis();
+  uint32_t now = MillisInternal::get();
   if (now - this->last_wdt_feed_ > WDT_FEED_INTERVAL_MS) {
     this->feed_wdt_slow_(now);
   }
@@ -288,7 +288,7 @@ void Application::run_powerdown_hooks() {
 }
 
 void Application::teardown_components(uint32_t timeout_ms) {
-  uint32_t start_time = millis();
+  uint32_t start_time = MillisInternal::get();
 
   // Use a StaticVector instead of std::vector to avoid heap allocation
   // since we know the actual size at compile time
@@ -367,7 +367,7 @@ void Application::teardown_components(uint32_t timeout_ms) {
     }
 
     // Update time for next iteration
-    now = millis();
+    now = MillisInternal::get();
   }
 
   if (pending_count > 0) {
@@ -410,7 +410,7 @@ void Application::disable_component_loop_(Component *component) {
           // This prevents integer underflow in timing calculations by ensuring
           // the swapped component starts with a fresh timing reference, avoiding
           // errors caused by stale or wrapped timing values.
-          this->loop_component_start_time_ = millis();
+          this->loop_component_start_time_ = MillisInternal::get();
         }
       }
       return;
diff --git a/esphome/core/scheduler.h b/esphome/core/scheduler.h
index 0372e06066..432a488a38 100644
--- a/esphome/core/scheduler.h
+++ b/esphome/core/scheduler.h
@@ -284,12 +284,14 @@ class Scheduler {
   bool cancel_retry_(Component *component, NameType name_type, const char *static_name, uint32_t hash_or_id);
 
   // Extend a 32-bit millis() value to 64-bit. Use when the caller already has a fresh now.
-  // On platforms with native 64-bit time (ESP32), ignores now and uses millis_64() directly.
-  // This means the Scheduler uses the esp_timer clock (via millis_64()) for all scheduling,
-  // even though the caller's 32-bit now came from xTaskGetTickCount (via millis()). Safe
-  // because scheduling only compares millis_64 against millis_64 — never against millis().
-  // On other platforms (ESP8266), extends now to 64-bit using rollover tracking, so both
-  // millis() and scheduling use the same clock.
+  // On platforms with native 64-bit time (ESP32, Host, Zephyr, RP2040 — see
+  // USE_NATIVE_64BIT_TIME in defines.h), ignores now and uses millis_64() directly, so the
+  // Scheduler always works in 64-bit time regardless of what the caller's 32-bit now came
+  // from. On ESP32 specifically, millis() comes from xTaskGetTickCount while millis_64()
+  // comes from esp_timer — two different clocks — but that is safe because scheduling
+  // compares millis_64 values against millis_64 only, never against millis().
+  // On platforms without native 64-bit time (e.g. ESP8266), extends now to 64-bit using
+  // rollover tracking, so both millis() and scheduling use the same underlying clock.
   uint64_t ESPHOME_ALWAYS_INLINE millis_64_from_(uint32_t now) {
 #ifdef USE_NATIVE_64BIT_TIME
     (void) now;