diff --git a/setup/dns.sh b/setup/dns.sh
index 855ff0c2..c8a73a73 100755
--- a/setup/dns.sh
+++ b/setup/dns.sh
@@ -62,8 +62,14 @@ for ip in $PRIVATE_IP $PRIVATE_IPV6; do
 	echo "  ip-address: $ip" >> /etc/nsd/nsd.conf;
 done
 
+# Create a directory for additional configuration directives, including
+# the zones.conf file written out by our management daemon.
 echo "include: /etc/nsd/nsd.conf.d/*.conf" >> /etc/nsd/nsd.conf;
 
+# Remove the old location of zones.conf that we generate. It will
+# now be stored in /etc/nsd/nsd.conf.d.
+rm -f /etc/nsd/zones.conf
+
 # Create DNSSEC signing keys.
 
 mkdir -p "$STORAGE_ROOT/dns/dnssec";