diff --git a/arch/x86/kernel/apic/io_apic.c b/arch/x86/kernel/apic/io_apic.c
index 3d8ff40ecc6f..7249f1500bcb 100644
--- a/arch/x86/kernel/apic/io_apic.c
+++ b/arch/x86/kernel/apic/io_apic.c
@@ -2118,6 +2118,7 @@ static inline void __init check_timer(void)
 			if (idx != -1 && irq_trigger(idx))
 				unmask_ioapic_irq(irq_get_chip_data(0));
 		}
+		irq_domain_deactivate_irq(irq_data);
 		irq_domain_activate_irq(irq_data);
 		if (timer_irq_works()) {
 			if (disable_timer_pin_1 > 0)
@@ -2139,6 +2140,7 @@ static inline void __init check_timer(void)
 		 * legacy devices should be connected to IO APIC #0
 		 */
 		replace_pin_at_irq_node(data, node, apic1, pin1, apic2, pin2);
+		irq_domain_deactivate_irq(irq_data);
 		irq_domain_activate_irq(irq_data);
 		legacy_pic->unmask(0);
 		if (timer_irq_works()) {
diff --git a/arch/x86/kernel/hpet.c b/arch/x86/kernel/hpet.c
index 274fab99169d..932348fbb6ea 100644
--- a/arch/x86/kernel/hpet.c
+++ b/arch/x86/kernel/hpet.c
@@ -352,6 +352,7 @@ static int hpet_resume(struct clock_event_device *evt, int timer)
 	} else {
 		struct hpet_dev *hdev = EVT_TO_HPET_DEV(evt);
 
+		irq_domain_deactivate_irq(irq_get_irq_data(hdev->irq));
 		irq_domain_activate_irq(irq_get_irq_data(hdev->irq));
 		disable_irq(hdev->irq);
 		irq_set_affinity(hdev->irq, cpumask_of(hdev->cpu));