diff --git a/cpu/saml1x/cpu.c b/cpu/saml1x/cpu.c
index c5c5693484..24c246bf6e 100644
--- a/cpu/saml1x/cpu.c
+++ b/cpu/saml1x/cpu.c
@@ -135,9 +135,21 @@ void cpu_init(void)
 #endif
 #ifdef MODULE_PERIPH_GPIO
                          | MCLK_APBAMASK_PORT
+#endif
+#ifdef MODULE_PERIPH_RTC_RTT
+                         | MCLK_APBAMASK_RTC
 #endif
                          ;
 
+
+    /* Disable the RTC module to prevent synchronization issues during CPU init
+       if the RTC was running from a previous boot (e.g wakeup from backup)
+       as the module will be re-init during the boot process */
+    if (RTC->MODE2.CTRLA.bit.ENABLE && IS_ACTIVE(MODULE_PERIPH_RTC_RTT)) {
+        while (RTC->MODE2.SYNCBUSY.reg) {}
+        RTC->MODE2.CTRLA.bit.ENABLE = 0;
+        while (RTC->MODE2.SYNCBUSY.reg) {}
+    }
     /* Software reset the GCLK module to ensure it is re-initialized correctly */
     GCLK->CTRLA.reg = GCLK_CTRLA_SWRST;
     while (GCLK->CTRLA.reg & GCLK_CTRLA_SWRST) {}