diff --git a/puppet/templates/puppet.conf.erb b/puppet/templates/puppet.conf.erb
index b7d688c..d214146 100644
--- a/puppet/templates/puppet.conf.erb
+++ b/puppet/templates/puppet.conf.erb
@@ -41,6 +41,10 @@
 
 <% if puppetversion[/\d+/].to_i >= 2 -%>
 [agent]
+    # Ignore site manifest when run as agent. Fixes warnings about
+    # storeconfigs on master.
+    manifest = /dev/null
+
 <% else -%>
 [puppetd]
 <% end -%>