diff --git a/pygit2/__init__.py b/pygit2/__init__.py
index 0a901d4..6df8478 100644
--- a/pygit2/__init__.py
+++ b/pygit2/__init__.py
@@ -151,6 +151,9 @@ def clone_repository(
     d['callback'] = credentials
     d_handle = ffi.new_handle(d)
 
+    # Perform the initialization with the version we compiled
+    C.git_clone_init_options(opts, C.GIT_CLONE_OPTIONS_VERSION)
+
     # We need to keep the ref alive ourselves
     checkout_branch_ref = None
     if branch:
@@ -160,11 +163,8 @@ def clone_repository(
     remote_name_ref = ffi.new('char []', to_bytes(remote_name))
     opts.remote_name = remote_name_ref
 
-    opts.version = 1
     opts.ignore_cert_errors = ignore_cert_errors
     opts.bare = bare
-    opts.remote_callbacks.version = 1
-    opts.checkout_opts.version = 1
     if credentials:
         opts.remote_callbacks.credentials = _credentials_cb
         opts.remote_callbacks.payload = d_handle
diff --git a/pygit2/decl.h b/pygit2/decl.h
index c7b7001..b8cd9c6 100644
--- a/pygit2/decl.h
+++ b/pygit2/decl.h
@@ -353,6 +353,9 @@ typedef struct git_clone_options {
 	git_signature *signature;
 } git_clone_options;
 
+#define GIT_CLONE_OPTIONS_VERSION ...
+int git_clone_init_options(git_clone_options *opts, unsigned int version);
+
 int git_clone(git_repository **out,
 	const char *url,
 	const char *local_path,