diff --git a/homeassistant/config_entries.py b/homeassistant/config_entries.py
index a41f4f24701..0d4cc5fd102 100644
--- a/homeassistant/config_entries.py
+++ b/homeassistant/config_entries.py
@@ -1507,10 +1507,14 @@ class ConfigEntriesFlowManager(
             version=result["version"],
         )
 
+        if existing_entry is not None:
+            # Unload and remove the existing entry
+            await self.config_entries._async_remove(existing_entry.entry_id)  # noqa: SLF001
         await self.config_entries.async_add(entry)
 
         if existing_entry is not None:
-            await self.config_entries.async_remove(existing_entry.entry_id)
+            # Clean up devices and entities belonging to the existing entry
+            self.config_entries._async_clean_up(existing_entry)  # noqa: SLF001
 
         result["result"] = entry
         return result
@@ -1900,7 +1904,21 @@ class ConfigEntries:
         self._async_schedule_save()
 
     async def async_remove(self, entry_id: str) -> dict[str, Any]:
-        """Remove an entry."""
+        """Remove, unload and clean up after an entry."""
+        unload_success, entry = await self._async_remove(entry_id)
+        self._async_clean_up(entry)
+
+        for discovery_domain in entry.discovery_keys:
+            async_dispatcher_send_internal(
+                self.hass,
+                signal_discovered_config_entry_removed(discovery_domain),
+                entry,
+            )
+
+        return {"require_restart": not unload_success}
+
+    async def _async_remove(self, entry_id: str) -> tuple[bool, ConfigEntry]:
+        """Remove and unload an entry."""
         if (entry := self.async_get_entry(entry_id)) is None:
             raise UnknownEntry
 
@@ -1916,6 +1934,13 @@ class ConfigEntries:
             self.async_update_issues()
             self._async_schedule_save()
 
+        return (unload_success, entry)
+
+    @callback
+    def _async_clean_up(self, entry: ConfigEntry) -> None:
+        """Clean up after an entry."""
+        entry_id = entry.entry_id
+
         dev_reg = device_registry.async_get(self.hass)
         ent_reg = entity_registry.async_get(self.hass)
 
@@ -1934,13 +1959,6 @@ class ConfigEntries:
                 ir.async_delete_issue(self.hass, HOMEASSISTANT_DOMAIN, issue_id)
 
         self._async_dispatch(ConfigEntryChange.REMOVED, entry)
-        for discovery_domain in entry.discovery_keys:
-            async_dispatcher_send_internal(
-                self.hass,
-                signal_discovered_config_entry_removed(discovery_domain),
-                entry,
-            )
-        return {"require_restart": not unload_success}
 
     @callback
     def _async_shutdown(self, event: Event) -> None: