diff --git a/src/knot/dnssec/nsec-chain.h b/src/knot/dnssec/nsec-chain.h
index b0c7fa7640821b98622515c7d697820d730d4e0c..dfdbeb55bf507fba75e2710bb2df6c37d9e532a1 100644
--- a/src/knot/dnssec/nsec-chain.h
+++ b/src/knot/dnssec/nsec-chain.h
@@ -54,7 +54,7 @@ inline static void bitmap_add_node_rrsets(dnssec_nsec_bitmap_t *bitmap,
                                           const zone_node_t *node)
 {
 	bool deleg = node->flags & NODE_FLAGS_DELEG;
-	bool apex = node->parent == NULL;
+	bool apex = node->flags & NODE_FLAGS_APEX;
 	for (int i = 0; i < node->rrset_count; i++) {
 		knot_rrset_t rr = node_rrset_at(node, i);
 		if (deleg && (rr.type != KNOT_RRTYPE_NS && rr.type != KNOT_RRTYPE_DS)) {
diff --git a/src/knot/dnssec/nsec3-chain.c b/src/knot/dnssec/nsec3-chain.c
index fe706af0c3b7ed61036fd148f1822ec61358041a..1012d2307b43e575b54415f48ebab0ba3a9a3999 100644
--- a/src/knot/dnssec/nsec3-chain.c
+++ b/src/knot/dnssec/nsec3-chain.c
@@ -698,7 +698,7 @@ static int nsec3_mark_empty(zone_node_t **node_p, void *data)
 		 */
 		node->flags |= NODE_FLAGS_EMPTY;
 
-		if (node->parent) {
+		if (!(node->flags & NODE_FLAGS_APEX)) {
 			/* We must decrease the parent's children count,
 			 * but only temporarily! It must be set back right after
 			 * the operation
diff --git a/src/knot/zone/adjust.c b/src/knot/zone/adjust.c
index 0a08e56aec2d278cdbcb646f91929057ea751a7e..6072142aa83acd2467061b3f1e8e217462e00460 100644
--- a/src/knot/zone/adjust.c
+++ b/src/knot/zone/adjust.c
@@ -38,7 +38,7 @@ int adjust_cb_flags(zone_node_t *node, const zone_contents_t *zone)
 		node->flags |= NODE_FLAGS_DELEG;
 	} else {
 		// Default.
-		node->flags = NODE_FLAGS_AUTH;
+		node->flags = NODE_FLAGS_AUTH | (node->flags & NODE_FLAGS_APEX);
 	}
 
 	return KNOT_EOK; // always returns this value :)
diff --git a/src/knot/zone/contents.c b/src/knot/zone/contents.c
index 48eea2f3878e7e1170b6ba797123a8bbc356e491..3f8b65014a3806a63e4a1541a18dc033bb20a943 100644
--- a/src/knot/zone/contents.c
+++ b/src/knot/zone/contents.c
@@ -162,6 +162,7 @@ zone_contents_t *zone_contents_new(const knot_dname_t *apex_name)
 	if (zone_tree_insert(contents->nodes, contents->apex) != KNOT_EOK) {
 		goto cleanup;
 	}
+	contents->apex->flags |= NODE_FLAGS_APEX;
 
 	return contents;
 
diff --git a/src/knot/zone/node.h b/src/knot/zone/node.h
index cb19f475de35496557e432abbf17450d41b37c60..8a77bae6e424ee0ab333ba45f7c82f12222adce9 100644
--- a/src/knot/zone/node.h
+++ b/src/knot/zone/node.h
@@ -81,6 +81,8 @@ enum node_flags {
 	NODE_FLAGS_WILDCARD_CHILD =  1 << 4,
 	/*! \brief Is this NSEC3 node compatible with zone's NSEC3PARAMS ? */
 	NODE_FLAGS_IN_NSEC3_CHAIN =  1 << 5,
+	/*! \brief Node is the zone Apex. */
+	NODE_FLAGS_APEX =            1 << 6,
 };
 
 /*!
diff --git a/src/knot/zone/semantic-check.c b/src/knot/zone/semantic-check.c
index 2ab3a83dbf91aa3a510414b8eceabe8219844214..eda497dc51be0bacfd468efe170e5c055fc5bec8 100644
--- a/src/knot/zone/semantic-check.c
+++ b/src/knot/zone/semantic-check.c
@@ -1093,7 +1093,7 @@ static int check_dname(const zone_node_t *node, semchecks_data_t *data)
 	}
 
 	/* RFC 6672 Section 2.3 Paragraph 3 */
-	bool is_apex = (node->parent == NULL);
+	bool is_apex = (node->flags & NODE_FLAGS_APEX);
 	if (!is_apex && node_rrtype_exists(node, KNOT_RRTYPE_NS)) {
 		data->handler->fatal_error = true;
 		data->handler->cb(data->handler, data->zone, node,
diff --git a/src/knot/zone/zone-tree.c b/src/knot/zone/zone-tree.c
index 486853bfb41ca01fa1052a4833818312b33f568b..85aa4c762bf1a4dc508a939feed0ebd27e5a10cb 100644
--- a/src/knot/zone/zone-tree.c
+++ b/src/knot/zone/zone-tree.c
@@ -154,7 +154,7 @@ void zone_tree_delete_empty(zone_tree_t *tree, zone_node_t *node)
 		if (parent_node != NULL) {
 			parent_node->children--;
 			fix_wildcard_child(parent_node, node->owner);
-			if (parent_node->parent != NULL) { /* Is not apex */
+			if (!(parent_node->flags & NODE_FLAGS_APEX)) { /* Is not apex */
 				// Recurse using the parent node, do not delete possibly empty parent.
 				zone_tree_delete_empty(tree, parent_node);
 			}