diff --git a/hw/xen/xen_pt_config_init.c b/hw/xen/xen_pt_config_init.c
index 8ccc2e4b9c..de9a20f437 100644
--- a/hw/xen/xen_pt_config_init.c
+++ b/hw/xen/xen_pt_config_init.c
@@ -1123,8 +1123,8 @@ static int xen_pt_msgctrl_reg_write(XenPCIPassthroughState *s,
             msi->mapped = true;
         }
         msi->flags |= PCI_MSI_FLAGS_ENABLE;
-    } else {
-        msi->flags &= ~PCI_MSI_FLAGS_ENABLE;
+    } else if (msi->mapped) {
+        xen_pt_msi_disable(s);
     }
 
     /* pass through MSI_ENABLE bit */
@@ -1397,6 +1397,8 @@ static int xen_pt_msixctrl_reg_write(XenPCIPassthroughState *s,
     if ((*val & PCI_MSIX_FLAGS_ENABLE)
         && !(*val & PCI_MSIX_FLAGS_MASKALL)) {
         xen_pt_msix_update(s);
+    } else if (!(*val & PCI_MSIX_FLAGS_ENABLE) && s->msix->enabled) {
+        xen_pt_msix_disable(s);
     }
 
     debug_msix_enabled_old = s->msix->enabled;
diff --git a/hw/xen/xen_pt_msi.c b/hw/xen/xen_pt_msi.c
index 6fbe0cc86b..12b4c4560c 100644
--- a/hw/xen/xen_pt_msi.c
+++ b/hw/xen/xen_pt_msi.c
@@ -282,7 +282,8 @@ void xen_pt_msi_disable(XenPCIPassthroughState *s)
                      msi->initialized);
 
     /* clear msi info */
-    msi->flags = 0;
+    msi->flags &= ~PCI_MSI_FLAGS_ENABLE;
+    msi->initialized = false;
     msi->mapped = false;
     msi->pirq = XEN_PT_UNASSIGNED_PIRQ;
 }
@@ -446,7 +447,8 @@ static void pci_msix_write(void *opaque, hwaddr addr,
     if (offset != PCI_MSIX_ENTRY_VECTOR_CTRL) {
         const volatile uint32_t *vec_ctrl;
 
-        if (get_entry_value(entry, offset) == val) {
+        if (get_entry_value(entry, offset) == val
+            && entry->pirq != XEN_PT_UNASSIGNED_PIRQ) {
             return;
         }