diff --git a/homeassistant/components/homekit_controller/__init__.py b/homeassistant/components/homekit_controller/__init__.py
index c863da14a3a..444f64b6f38 100644
--- a/homeassistant/components/homekit_controller/__init__.py
+++ b/homeassistant/components/homekit_controller/__init__.py
@@ -9,8 +9,7 @@ from homeassistant.exceptions import ConfigEntryNotReady
 from homeassistant.helpers import device_registry as dr
 from homeassistant.helpers.entity import Entity
 
-# We need an import from .config_flow, without it .config_flow is never loaded.
-from .config_flow import HomekitControllerFlowHandler  # noqa: F401
+from .config_flow import normalize_hkid
 from .connection import HKDevice, get_accessory_information
 from .const import CONTROLLER, DOMAIN, ENTITY_MAP, KNOWN_DEVICES
 from .storage import EntityMapStorage
@@ -181,6 +180,12 @@ async def async_setup_entry(hass, entry):
     conn = HKDevice(hass, entry, entry.data)
     hass.data[KNOWN_DEVICES][conn.unique_id] = conn
 
+    # For backwards compat
+    if entry.unique_id is None:
+        hass.config_entries.async_update_entry(
+            entry, unique_id=normalize_hkid(conn.unique_id)
+        )
+
     if not await conn.async_setup():
         del hass.data[KNOWN_DEVICES][conn.unique_id]
         raise ConfigEntryNotReady
diff --git a/homeassistant/components/homekit_controller/config_flow.py b/homeassistant/components/homekit_controller/config_flow.py
index f4eb1190727..6cc724e9fe5 100644
--- a/homeassistant/components/homekit_controller/config_flow.py
+++ b/homeassistant/components/homekit_controller/config_flow.py
@@ -46,6 +46,11 @@ def load_old_pairings(hass):
     return old_pairings
 
 
+def normalize_hkid(hkid):
+    """Normalize a hkid so that it is safe to compare with other normalized hkids."""
+    return hkid.lower()
+
+
 @callback
 def find_existing_host(hass, serial):
     """Return a set of the configured hosts."""
@@ -77,6 +82,9 @@ class HomekitControllerFlowHandler(config_entries.ConfigFlow):
             key = user_input["device"]
             self.hkid = self.devices[key]["id"]
             self.model = self.devices[key]["md"]
+            await self.async_set_unique_id(
+                normalize_hkid(self.hkid), raise_on_progress=False
+            )
             return await self.async_step_pair()
 
         all_hosts = await self.hass.async_add_executor_job(self.controller.discover, 5)
@@ -120,18 +128,6 @@ class HomekitControllerFlowHandler(config_entries.ConfigFlow):
         status_flags = int(properties["sf"])
         paired = not status_flags & 0x01
 
-        _LOGGER.debug("Discovered device %s (%s - %s)", name, model, hkid)
-
-        # pylint: disable=no-member # https://github.com/PyCQA/pylint/issues/3167
-        self.context["hkid"] = hkid
-        self.context["title_placeholders"] = {"name": name}
-
-        # If multiple HomekitControllerFlowHandler end up getting created
-        # for the same accessory dont  let duplicates hang around
-        active_flows = self._async_in_progress()
-        if any(hkid == flow["context"]["hkid"] for flow in active_flows):
-            return self.async_abort(reason="already_in_progress")
-
         # The configuration number increases every time the characteristic map
         # needs updating. Some devices use a slightly off-spec name so handle
         # both cases.
@@ -143,21 +139,27 @@ class HomekitControllerFlowHandler(config_entries.ConfigFlow):
             )
             config_num = None
 
-        if paired:
-            if hkid in self.hass.data.get(KNOWN_DEVICES, {}):
-                # The device is already paired and known to us
-                # According to spec we should monitor c# (config_num) for
-                # changes. If it changes, we check for new entities
-                conn = self.hass.data[KNOWN_DEVICES][hkid]
-                if conn.config_num != config_num:
-                    _LOGGER.debug(
-                        "HomeKit info %s: c# incremented, refreshing entities", hkid
-                    )
-                    self.hass.async_create_task(
-                        conn.async_refresh_entity_map(config_num)
-                    )
-                return self.async_abort(reason="already_configured")
+        # If the device is already paired and known to us we should monitor c#
+        # (config_num) for changes. If it changes, we check for new entities
+        if paired and hkid in self.hass.data.get(KNOWN_DEVICES, {}):
+            conn = self.hass.data[KNOWN_DEVICES][hkid]
+            if conn.config_num != config_num:
+                _LOGGER.debug(
+                    "HomeKit info %s: c# incremented, refreshing entities", hkid
+                )
+                self.hass.async_create_task(conn.async_refresh_entity_map(config_num))
+            return self.async_abort(reason="already_configured")
 
+        _LOGGER.debug("Discovered device %s (%s - %s)", name, model, hkid)
+
+        await self.async_set_unique_id(normalize_hkid(hkid))
+        self._abort_if_unique_id_configured()
+
+        # pylint: disable=no-member # https://github.com/PyCQA/pylint/issues/3167
+        self.context["hkid"] = hkid
+        self.context["title_placeholders"] = {"name": name}
+
+        if paired:
             old_pairings = await self.hass.async_add_executor_job(
                 load_old_pairings, self.hass
             )
diff --git a/tests/components/homekit_controller/test_config_flow.py b/tests/components/homekit_controller/test_config_flow.py
index 22b486e1d51..4733581f136 100644
--- a/tests/components/homekit_controller/test_config_flow.py
+++ b/tests/components/homekit_controller/test_config_flow.py
@@ -74,6 +74,7 @@ async def test_discovery_works(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device enters pairing mode and displays code
@@ -122,6 +123,7 @@ async def test_discovery_works_upper_case(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device enters pairing mode and displays code
@@ -169,6 +171,7 @@ async def test_discovery_works_missing_csharp(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device enters pairing mode and displays code
@@ -234,6 +237,7 @@ async def test_pair_already_paired_1(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -259,6 +263,7 @@ async def test_discovery_ignored_model(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -286,6 +291,7 @@ async def test_discovery_invalid_config_entry(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # Discovery of a HKID that is in a pairable state but for which there is
@@ -315,10 +321,7 @@ async def test_discovery_already_configured(hass):
     result = await flow.async_step_zeroconf(discovery_info)
     assert result["type"] == "abort"
     assert result["reason"] == "already_configured"
-    assert flow.context == {
-        "hkid": "00:00:00:00:00:00",
-        "title_placeholders": {"name": "TestDevice"},
-    }
+    assert flow.context == {}
 
     assert conn.async_config_num_changed.call_count == 0
 
@@ -343,10 +346,7 @@ async def test_discovery_already_configured_config_change(hass):
     result = await flow.async_step_zeroconf(discovery_info)
     assert result["type"] == "abort"
     assert result["reason"] == "already_configured"
-    assert flow.context == {
-        "hkid": "00:00:00:00:00:00",
-        "title_placeholders": {"name": "TestDevice"},
-    }
+    assert flow.context == {}
 
     assert conn.async_refresh_entity_map.call_args == mock.call(2)
 
@@ -369,6 +369,7 @@ async def test_pair_unable_to_pair(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device enters pairing mode and displays code
@@ -402,6 +403,7 @@ async def test_pair_abort_errors_on_start(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device refuses to enter pairing mode
@@ -414,6 +416,7 @@ async def test_pair_abort_errors_on_start(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -436,6 +439,7 @@ async def test_pair_form_errors_on_start(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device refuses to enter pairing mode
@@ -448,6 +452,7 @@ async def test_pair_form_errors_on_start(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -470,6 +475,7 @@ async def test_pair_abort_errors_on_finish(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device enters pairing mode and displays code
@@ -486,6 +492,7 @@ async def test_pair_abort_errors_on_finish(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -508,6 +515,7 @@ async def test_pair_form_errors_on_finish(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
     # User initiates pairing - device enters pairing mode and displays code
@@ -524,6 +532,7 @@ async def test_pair_form_errors_on_finish(hass, exception, expected):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -712,6 +721,7 @@ async def test_parse_new_homekit_json(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -763,6 +773,7 @@ async def test_parse_old_homekit_json(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }
 
 
@@ -823,4 +834,5 @@ async def test_parse_overlapping_homekit_json(hass):
     assert flow.context == {
         "hkid": "00:00:00:00:00:00",
         "title_placeholders": {"name": "TestDevice"},
+        "unique_id": "00:00:00:00:00:00",
     }