diff --git a/cpu/sam0_common/periph/gpio_ll_irq.c b/cpu/sam0_common/periph/gpio_ll_irq.c
index e1b426034702..98304c5a8cce 100644
--- a/cpu/sam0_common/periph/gpio_ll_irq.c
+++ b/cpu/sam0_common/periph/gpio_ll_irq.c
@@ -181,8 +181,11 @@ void gpio_ll_irq_unmask_and_clear(gpio_port_t port, uint8_t pin)
     int exti_num = get_exti_num(port_num, pin);
     assume(exti_num >= 0);
 
-    EIC_SEC->INTENSET.reg = 1U << exti_num;
-    EIC_SEC->INTFLAG.reg = 1U << exti_num;
+    unsigned irq_state = irq_disable();
+    uint32_t mask = 1U << exti_num;
+    EIC_SEC->INTFLAG.reg = mask;
+    EIC_SEC->INTENSET.reg = mask;
+    irq_restore(irq_state);
 }
 
 int gpio_ll_irq(gpio_port_t port, uint8_t pin, gpio_irq_trig_t trig,