diff --git a/doc/Makefile b/doc/Makefile
index 8fbbefbd..2ab5a5ce 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -9,6 +9,14 @@ SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
 
+# Require stricter builds with
+#   -n: warn on missing references
+#   -W: error on warnings
+#   --keep-going: find all warnings
+# https://www.sphinx-doc.org/en/master/man/sphinx-build.html
+STRICT = -n -W --keep-going
+LOOSE = -n
+
 GENERATE = ../devel/generate-command-doc
 
 # Put it first so that "make" without argument is like "make help".
@@ -21,7 +29,7 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	if [[ $@ != clean ]]; then $(GENERATE); fi
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(STRICT) $(SPHINXOPTS) $(O)
 
 HOST ?= 127.0.0.1
 PORT ?= 8000
@@ -30,4 +38,4 @@ serve: dirhtml
 	cd "$(BUILDDIR)/dirhtml" && python3 -m http.server --bind "$(HOST)" "$(PORT)"
 
 livehtml:
-	sphinx-autobuild -b dirhtml "$(SOURCEDIR)" "$(BUILDDIR)/dirhtml" --host "$(HOST)" --port "$(PORT)" --watch ../nextstrain/cli --pre-build "$(GENERATE)" $(SPHINXOPTS) $(O)
+	sphinx-autobuild -b dirhtml "$(SOURCEDIR)" "$(BUILDDIR)/dirhtml" --host "$(HOST)" --port "$(PORT)" --watch ../nextstrain/cli --pre-build "$(GENERATE)" $(LOOSE) $(SPHINXOPTS) $(O)