diff --git a/src/libexpr/common-eval-args.cc b/src/libexpr/common-eval-args.cc
index 7c0d268bd..e3135b472 100644
--- a/src/libexpr/common-eval-args.cc
+++ b/src/libexpr/common-eval-args.cc
@@ -3,6 +3,8 @@
 #include "download.hh"
 #include "util.hh"
 #include "eval.hh"
+#include "fetchers/registry.hh"
+#include "flake/flakeref.hh"
 
 namespace nix {
 
@@ -40,7 +42,9 @@ MixEvalArgs::MixEvalArgs()
       .description("override a flake registry value")
       .arity(2)
       .handler([&](std::vector<std::string> ss) {
-          registryOverrides.push_back(std::make_pair(ss[0], ss[1]));
+          fetchers::overrideRegistry(
+              parseFlakeRef(ss[0], absPath(".")).input,
+              parseFlakeRef(ss[1], absPath(".")).input);
       });
 }
 
diff --git a/src/libexpr/common-eval-args.hh b/src/libexpr/common-eval-args.hh
index 54fb731de..be7fda783 100644
--- a/src/libexpr/common-eval-args.hh
+++ b/src/libexpr/common-eval-args.hh
@@ -16,8 +16,6 @@ struct MixEvalArgs : virtual Args
 
     Strings searchPath;
 
-    std::vector<std::pair<std::string, std::string>> registryOverrides;
-
 private:
 
     std::map<std::string, std::string> autoArgs;
diff --git a/src/libstore/fetchers/registry.cc b/src/libstore/fetchers/registry.cc
index dd74e16c1..9c74f118d 100644
--- a/src/libstore/fetchers/registry.cc
+++ b/src/libstore/fetchers/registry.cc
@@ -11,11 +11,10 @@ namespace nix::fetchers {
 std::shared_ptr<Registry> Registry::read(
     const Path & path, RegistryType type)
 {
-    auto registry = std::make_shared<Registry>();
-    registry->type = type;
+    auto registry = std::make_shared<Registry>(type);
 
     if (!pathExists(path))
-        return std::make_shared<Registry>();
+        return std::make_shared<Registry>(type);
 
     auto json = nlohmann::json::parse(readFile(path));
 
@@ -74,17 +73,20 @@ std::shared_ptr<Registry> getUserRegistry()
     return Registry::read(getUserRegistryPath(), Registry::User);
 }
 
-#if 0
-std::shared_ptr<Registry> getFlagRegistry(RegistryOverrides registryOverrides)
+static std::shared_ptr<Registry> flagRegistry =
+    std::make_shared<Registry>(Registry::Flag);
+
+std::shared_ptr<Registry> getFlagRegistry()
 {
-    auto flagRegistry = std::make_shared<Registry>();
-    for (auto const & x : registryOverrides)
-        flagRegistry->entries.insert_or_assign(
-            parseFlakeRef2(x.first),
-            parseFlakeRef2(x.second));
     return flagRegistry;
 }
-#endif
+
+void overrideRegistry(
+    const std::shared_ptr<const Input> & from,
+    const std::shared_ptr<const Input> & to)
+{
+    flagRegistry->add(from, to);
+}
 
 static std::shared_ptr<Registry> getGlobalRegistry(ref<Store> store)
 {
@@ -107,7 +109,7 @@ static std::shared_ptr<Registry> getGlobalRegistry(ref<Store> store)
 Registries getRegistries(ref<Store> store)
 {
     Registries registries;
-    //registries.push_back(getFlagRegistry(registryOverrides));
+    registries.push_back(getFlagRegistry());
     registries.push_back(getUserRegistry());
     registries.push_back(getGlobalRegistry(store));
     return registries;
diff --git a/src/libstore/fetchers/registry.hh b/src/libstore/fetchers/registry.hh
index 1757ce323..e29f78486 100644
--- a/src/libstore/fetchers/registry.hh
+++ b/src/libstore/fetchers/registry.hh
@@ -20,6 +20,10 @@ struct Registry
 
     std::vector<std::pair<std::shared_ptr<const Input>, std::shared_ptr<const Input>>> entries;
 
+    Registry(RegistryType type)
+        : type(type)
+    { }
+
     static std::shared_ptr<Registry> read(
         const Path & path, RegistryType type);
 
@@ -40,6 +44,10 @@ Path getUserRegistryPath();
 
 Registries getRegistries(ref<Store> store);
 
+void overrideRegistry(
+    const std::shared_ptr<const Input> & from,
+    const std::shared_ptr<const Input> & to);
+
 std::shared_ptr<const Input> lookupInRegistries(
     ref<Store> store,
     std::shared_ptr<const Input> input);
diff --git a/tests/flakes.sh b/tests/flakes.sh
index 334f750fb..337645fb4 100644
--- a/tests/flakes.sh
+++ b/tests/flakes.sh
@@ -293,6 +293,13 @@ nix build -o $TEST_ROOT/result --flake-registry $registry flake3#xyzzy flake3#fn
 # Test doing multiple `lookupFlake`s
 nix build -o $TEST_ROOT/result --flake-registry $registry flake4#xyzzy
 
+# Test 'nix flake update' and --override-flake.
+nix flake update --flake-registry $registry $flake3Dir
+[[ -z $(git -C $flake3Dir diff master) ]]
+
+nix flake update --flake-registry $registry $flake3Dir --recreate-lock-file --override-flake flake2 nixpkgs
+[[ ! -z $(git -C $flake3Dir diff master) ]]
+
 # Make branch "removeXyzzy" where flake3 doesn't have xyzzy anymore
 git -C $flake3Dir checkout -b removeXyzzy
 rm $flake3Dir/flake.nix