diff --git a/esphome/components/preferences/__init__.py b/esphome/components/preferences/__init__.py
index 1da6d02045..c6bede891a 100644
--- a/esphome/components/preferences/__init__.py
+++ b/esphome/components/preferences/__init__.py
@@ -1,6 +1,8 @@
 import esphome.codegen as cg
 import esphome.config_validation as cv
 from esphome.const import CONF_ID
+from esphome.core import coroutine_with_priority
+from esphome.coroutine import CoroPriority
 
 CODEOWNERS = ["@esphome/core"]
 
@@ -16,6 +18,7 @@ CONFIG_SCHEMA = cv.Schema(
 ).extend(cv.COMPONENT_SCHEMA)
 
 
+@coroutine_with_priority(CoroPriority.PREFERENCES)
 async def to_code(config):
     var = cg.new_Pvariable(config[CONF_ID])
     cg.add(var.set_write_interval(config[CONF_FLASH_WRITE_INTERVAL]))
diff --git a/esphome/components/safe_mode/safe_mode.cpp b/esphome/components/safe_mode/safe_mode.cpp
index cd07f11cc5..c7bd8748f5 100644
--- a/esphome/components/safe_mode/safe_mode.cpp
+++ b/esphome/components/safe_mode/safe_mode.cpp
@@ -150,16 +150,6 @@ void SafeModeComponent::clean_rtc() {
   // remain incremented.
   uint32_t val = 0;
   this->rtc_.save(&val);
-#ifdef USE_LIBRETINY
-  // On LibreTiny (BK72xx, RTL87xx), preferences queued during shutdown are not
-  // reliably persisted to flash. This was observed on TuyaMCU devices where:
-  // 1. Safe mode button pressed or boot loop detected -> clean_rtc() queues counter=0
-  // 2. OTA completes -> safe_reboot() triggers IntervalSyncer::on_shutdown() -> sync()
-  // 3. After reboot, counter is NOT cleared -> device stuck in safe mode loop
-  // The FlashDB layer appears to fail silently when writing during shutdown.
-  // Sync immediately to ensure the boot counter is actually persisted.
-  global_preferences->sync();
-#endif
 }
 
 void SafeModeComponent::on_safe_shutdown() {
diff --git a/esphome/coroutine.py b/esphome/coroutine.py
index 0331c602c5..f5d512e510 100644
--- a/esphome/coroutine.py
+++ b/esphome/coroutine.py
@@ -114,6 +114,14 @@ class CoroPriority(enum.IntEnum):
     # Examples: web_server_ota (52)
     WEB_SERVER_OTA = 52
 
+    # Preferences - must run before APPLICATION (safe_mode) because safe_mode
+    # uses an early return when entering safe mode, skipping all lower priority
+    # component registration. Without IntervalSyncer registered, preferences
+    # cannot be synced during shutdown in safe mode, causing issues like the
+    # boot counter never being cleared and devices getting stuck in safe mode.
+    # Examples: preferences (51)
+    PREFERENCES = 51
+
     # Application-level services
     # Examples: safe_mode (50)
     APPLICATION = 50