diff --git a/scripts/addons_core/bl_pkg/bl_extension_ops.py b/scripts/addons_core/bl_pkg/bl_extension_ops.py
index fe6db77227b..b1026ac1377 100644
--- a/scripts/addons_core/bl_pkg/bl_extension_ops.py
+++ b/scripts/addons_core/bl_pkg/bl_extension_ops.py
@@ -56,6 +56,9 @@ rna_prop_enable_on_install = BoolProperty(
     name="Enable on Install",
     description="Enable after installing",
     default=True,
+    # This is done as "enabling" has security implications (running code after the action).
+    # Using the last value would mean an action that isn't expected to enable the extension might unintentionally do so.
+    options={'SKIP_SAVE'}
 )
 rna_prop_enable_on_install_type_map = {
     "add-on": "Enable Add-on",
@@ -1845,6 +1848,7 @@ class EXTENSIONS_OT_package_upgrade_all(Operator, _ExtCmdMixIn):
             if pkg_manifest_local is None:
                 continue
 
+            repo_item = repos_all[repo_index]
             for pkg_id, item_remote in pkg_manifest_remote.items():
                 item_local = pkg_manifest_local.get(pkg_id)
                 if item_local is None:
@@ -1858,8 +1862,11 @@ class EXTENSIONS_OT_package_upgrade_all(Operator, _ExtCmdMixIn):
                     packages_to_upgrade[repo_index].append(pkg_id)
                     package_count += 1
 
-            if packages_to_upgrade[repo_index]:
-                handle_addons_info.append((repos_all[repo_index], list(packages_to_upgrade[repo_index])))
+            if (pkg_id_sequence_upgrade := _preferences_pkg_id_sequence_filter_enabled(
+                    repo_item,
+                    packages_to_upgrade[repo_index],
+            )):
+                handle_addons_info.append((repo_item, pkg_id_sequence_upgrade))
 
         cmd_batch = []
         for repo_index, pkg_id_sequence in enumerate(packages_to_upgrade):
diff --git a/scripts/addons_core/bl_pkg/bl_extension_ui.py b/scripts/addons_core/bl_pkg/bl_extension_ui.py
index 455736f3abd..8973774b72c 100644
--- a/scripts/addons_core/bl_pkg/bl_extension_ui.py
+++ b/scripts/addons_core/bl_pkg/bl_extension_ui.py
@@ -1323,6 +1323,7 @@ def extension_draw_item(
                 props = row_right.operator("extensions.package_install", text="Update")
                 props.repo_index = repo_index
                 props.pkg_id = pkg_id
+                props.enable_on_install = is_enabled
                 del props
         else:
             props = row_right.operator("extensions.package_install", text="Install")