diff --git a/Makefile b/Makefile
index 95b18f0d..d8ef2bf4 100644
--- a/Makefile
+++ b/Makefile
@@ -65,12 +65,11 @@ coverage: ## check code coverage quickly with the default Python
 		$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/bigchaindb.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ bigchaindb
-	$(MAKE) -C docs clean
-	$(MAKE) -C docs html
-	$(BROWSER) docs/_build/html/index.html
+	$(MAKE) -C docs/root clean
+	$(MAKE) -C docs/root html
+	$(MAKE) -C docs/server clean
+	$(MAKE) -C docs/server html
+	$(BROWSER) docs/root/_build/html/index.html
 
 servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .