diff --git a/src/libexpr/flake/lockfile.cc b/src/libexpr/flake/lockfile.cc
index 3d796eadc..bf55b4e3b 100644
--- a/src/libexpr/flake/lockfile.cc
+++ b/src/libexpr/flake/lockfile.cc
@@ -8,18 +8,7 @@ namespace nix::flake {
 
 FlakeRef flakeRefFromJson(const nlohmann::json & json)
 {
-    fetchers::Input::Attrs attrs;
-
-    for (auto & i : json.items()) {
-        if (i.value().is_number())
-            attrs.emplace(i.key(), i.value().get<int64_t>());
-        else if (i.value().is_string())
-            attrs.emplace(i.key(), i.value().get<std::string>());
-        else
-            throw Error("unsupported input attribute type in lock file");
-    }
-
-    return FlakeRef::fromAttrs(attrs);
+    return FlakeRef::fromAttrs(jsonToAttrs(json));
 }
 
 FlakeRef getFlakeRef(
diff --git a/src/libstore/fetchers/fetchers.cc b/src/libstore/fetchers/fetchers.cc
index 373786f38..90bdc0fc5 100644
--- a/src/libstore/fetchers/fetchers.cc
+++ b/src/libstore/fetchers/fetchers.cc
@@ -37,6 +37,22 @@ std::unique_ptr<Input> inputFromAttrs(const Input::Attrs & attrs)
     throw Error("input '%s' is unsupported", attrsToJson(attrs));
 }
 
+Input::Attrs jsonToAttrs(const nlohmann::json & json)
+{
+    fetchers::Input::Attrs attrs;
+
+    for (auto & i : json.items()) {
+        if (i.value().is_number())
+            attrs.emplace(i.key(), i.value().get<int64_t>());
+        else if (i.value().is_string())
+            attrs.emplace(i.key(), i.value().get<std::string>());
+        else
+            throw Error("unsupported input attribute type in lock file");
+    }
+
+    return attrs;
+}
+
 nlohmann::json attrsToJson(const fetchers::Input::Attrs & attrs)
 {
     nlohmann::json json;
diff --git a/src/libstore/fetchers/fetchers.hh b/src/libstore/fetchers/fetchers.hh
index 9fafbffb6..4202e8339 100644
--- a/src/libstore/fetchers/fetchers.hh
+++ b/src/libstore/fetchers/fetchers.hh
@@ -98,6 +98,8 @@ std::unique_ptr<Input> inputFromAttrs(const Input::Attrs & attrs);
 
 void registerInputScheme(std::unique_ptr<InputScheme> && fetcher);
 
+Input::Attrs jsonToAttrs(const nlohmann::json & json);
+
 nlohmann::json attrsToJson(const Input::Attrs & attrs);
 
 std::optional<std::string> maybeGetStrAttr(const Input::Attrs & attrs, const std::string & name);
diff --git a/src/libstore/fetchers/registry.cc b/src/libstore/fetchers/registry.cc
index 9c74f118d..1fd42a169 100644
--- a/src/libstore/fetchers/registry.cc
+++ b/src/libstore/fetchers/registry.cc
@@ -19,31 +19,51 @@ std::shared_ptr<Registry> Registry::read(
     auto json = nlohmann::json::parse(readFile(path));
 
     auto version = json.value("version", 0);
-    if (version != 1)
+
+    // FIXME: remove soon
+    if (version == 1) {
+        auto flakes = json["flakes"];
+        for (auto i = flakes.begin(); i != flakes.end(); ++i) {
+            auto url = i->value("url", i->value("uri", ""));
+            if (url.empty())
+                throw Error("flake registry '%s' lacks a 'url' attribute for entry '%s'",
+                    path, i.key());
+            registry->entries.push_back(
+                {inputFromURL(i.key()), inputFromURL(url)});
+        }
+    }
+
+    else if (version == 2) {
+        for (auto & i : json["flakes"])
+            registry->entries.push_back(
+                { inputFromAttrs(jsonToAttrs(i["from"]))
+                , inputFromAttrs(jsonToAttrs(i["to"]))
+                });
+    }
+
+    else
         throw Error("flake registry '%s' has unsupported version %d", path, version);
 
-    auto flakes = json["flakes"];
-    for (auto i = flakes.begin(); i != flakes.end(); ++i) {
-        // FIXME: remove 'uri' soon.
-        auto url = i->value("url", i->value("uri", ""));
-        if (url.empty())
-            throw Error("flake registry '%s' lacks a 'url' attribute for entry '%s'",
-                path, i.key());
-        registry->entries.push_back(
-            {inputFromURL(i.key()), inputFromURL(url)});
-    }
 
     return registry;
 }
 
 void Registry::write(const Path & path)
 {
+    nlohmann::json arr;
+    for (auto & elem : entries) {
+        nlohmann::json obj;
+        obj["from"] = attrsToJson(elem.first->toAttrs());
+        obj["to"] = attrsToJson(elem.second->toAttrs());
+        arr.emplace_back(std::move(obj));
+    }
+
     nlohmann::json json;
-    json["version"] = 1;
-    for (auto & elem : entries)
-        json["flakes"][elem.first->to_string()] = { {"url", elem.second->to_string()} };
+    json["version"] = 2;
+    json["flakes"] = std::move(arr);
+
     createDirs(dirOf(path));
-    writeFile(path, json.dump(4));
+    writeFile(path, json.dump(2));
 }
 
 void Registry::add(
diff --git a/tests/flakes.sh b/tests/flakes.sh
index 434f5cb7a..6dbd534e0 100644
--- a/tests/flakes.sh
+++ b/tests/flakes.sh
@@ -94,27 +94,63 @@ git -C $nonFlakeDir commit -m 'Initial'
 
 cat > $registry <<EOF
 {
-    "flakes": {
-        "flake:flake1": {
-            "url": "git+file://$flake1Dir"
-        },
-        "flake:flake2": {
-            "url": "git+file://$flake2Dir"
-        },
-        "flake:flake3": {
-            "url": "git+file://$flake3Dir"
-        },
-        "flake:flake4": {
-            "url": "flake:flake3"
-        },
-        "flake:flake5": {
-            "url": "hg+file://$flake5Dir"
-        },
-        "flake:nixpkgs": {
-            "url": "flake:flake1"
-        }
+  "version": 2,
+  "flakes": [
+    { "from": {
+        "type": "indirect",
+        "id": "flake1"
+      },
+      "to": {
+        "type": "git",
+        "url": "file://$flake1Dir"
+      }
     },
-    "version": 1
+    { "from": {
+        "type": "indirect",
+        "id": "flake2"
+      },
+      "to": {
+        "type": "git",
+        "url": "file://$flake2Dir"
+      }
+    },
+    { "from": {
+        "type": "indirect",
+        "id": "flake3"
+      },
+      "to": {
+        "type": "git",
+        "url": "file://$flake3Dir"
+      }
+    },
+    { "from": {
+        "type": "indirect",
+        "id": "flake4"
+      },
+      "to": {
+        "type": "indirect",
+        "id": "flake3"
+      }
+    },
+    { "from": {
+        "type": "indirect",
+        "id": "flake5"
+      },
+      "to": {
+        "type": "hg",
+        "url": "file://$flake5Dir"
+      }
+    },
+    { "from": {
+        "type": "indirect",
+        "id": "nixpkgs"
+      },
+      "to": {
+        "type": "indirect",
+        "id": "flake1"
+      }
+    }
+  ]
 }
 EOF