diff --git a/drivers/pinctrl/pinctrl_ite_it8xxx2.c b/drivers/pinctrl/pinctrl_ite_it8xxx2.c
index 1416af04809..33b7075f02f 100644
--- a/drivers/pinctrl/pinctrl_ite_it8xxx2.c
+++ b/drivers/pinctrl/pinctrl_ite_it8xxx2.c
@@ -176,12 +176,14 @@ static int pinctrl_gpio_it8xxx2_configure_pins(const pinctrl_soc_pin_t *pins)
 	/*
 	 * Handle alternate function.
 	 */
-	if (reg_func3_gcr != NULL) {
-		*reg_func3_gcr &= ~gpio->func3_en_mask[pin];
-	}
-	/* Ensure that func3-ext setting is in default state. */
-	if (reg_func3_ext != NULL) {
-		*reg_func3_ext &= ~gpio->func3_ext_mask[pin];
+	if (pins->alt_func == IT8XXX2_ALT_FUNC_3) {
+		if (reg_func3_gcr != NULL) {
+			*reg_func3_gcr &= ~gpio->func3_en_mask[pin];
+		}
+		/* Ensure that func3-ext setting is in default state. */
+		if (reg_func3_ext != NULL) {
+			*reg_func3_ext &= ~gpio->func3_ext_mask[pin];
+		}
 	}
 
 	switch (pins->alt_func) {