diff --git a/cpu/sam0_common/periph/gpio.c b/cpu/sam0_common/periph/gpio.c
index a075e6a95b..e3de9c8e7a 100644
--- a/cpu/sam0_common/periph/gpio.c
+++ b/cpu/sam0_common/periph/gpio.c
@@ -322,6 +322,11 @@ void gpio_irq_enable(gpio_t pin)
     if (exti == -1) {
         return;
     }
+
+    /* clear stale interrupt */
+    _EIC->INTFLAG.reg = (1 << exti);
+
+    /* enable interrupt */
     _EIC->INTENSET.reg = (1 << exti);
 }