diff --git a/Makefile b/Makefile
index 5049d7f3c9f..200dbb68920 100644
--- a/Makefile
+++ b/Makefile
@@ -24,11 +24,11 @@ docs: ## generate Sphinx HTML documentation, including API docs
 	$(IN_VENV) $(MAKE) -C doc clean
 	$(IN_VENV) $(MAKE) -C doc html
 
-docs-schema-ready: ## Build Github-flavored Markdown from Galaxy Tool XSD
+docs-schema-ready: ## Build Github-flavored Markdown from Galaxy Tool XSD (expects libxml in environment)
 	python $(DOCS_DIR)/parse_gx_xsd.py > $(DOCS_DIR)/schema.md
 
-docs-schema-html: docs-schema-ready ## Convert Galaxy Tool XSD Markdown docs into HTML
-	markdown $(DOCS_DIR)/schema.md > $(DOCS_DIR)/schema.html
+docs-schema-html: docs-schema-ready ## Convert Galaxy Tool XSD Markdown docs into HTML (expects pandoc in environment)
+	pandoc $(DOCS_DIR)/schema.md -f markdown_github -s -o $(DOCS_DIR)/schema.html
 
 open-docs-schema: docs-schema-html ## Open HTML generated from Galaxy Tool XSD.
 	$(OPEN_RESOURCE) $(DOCS_DIR)/schema.html