diff --git a/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan.c b/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan.c
index fc85e67441e..37bc040b883 100644
--- a/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan.c
+++ b/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan.c
@@ -1549,6 +1549,11 @@ static int isr_rx_scan_report(struct lll_scan *lll, uint8_t devmatch_ok,
 			{
 				struct node_rx_ftr *ftr;
 
+				/* Reset Scan context association with any Aux context as a new
+				 * extended advertising chain is being setup for reception here.
+				 */
+				lll->lll_aux = NULL;
+
 				ftr = &(node_rx->rx_ftr);
 				ftr->param = lll;
 				ftr->ticks_anchor = radio_tmr_start_get();
diff --git a/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan_aux.c b/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan_aux.c
index 2424ab8a653..8f913558aea 100644
--- a/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan_aux.c
+++ b/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_scan_aux.c
@@ -1241,17 +1241,32 @@ static int isr_rx_pdu(struct lll_scan *lll, struct lll_scan_aux *lll_aux,
 
 		ftr = &(node_rx->rx_ftr);
 		if (lll_aux) {
+			/* Auxiliary context was used in ULL scheduling in the
+			 * reception of this current PDU.
+			 */
 			ftr->param = lll_aux;
 			ftr->scan_rsp = lll_aux->state;
 
 			/* Further auxiliary PDU reception will be chain PDUs */
 			lll_aux->is_chain_sched = 1U;
+
+			/* Reset auxiliary context association with scan context
+			 * as ULL scheduling has been used and may switch to
+			 * using LLL scheduling if the next auxiliary PDU in
+			 * chain is below the threshold to use ULL scheduling.
+			 */
+			lll->lll_aux = NULL;
+
 		} else if (lll->lll_aux) {
+			/* Auxiliary context was allocated to Scan context in
+			 * LLL scheduling in the reception of this current PDU.
+			 */
 			ftr->param = lll;
 			ftr->scan_rsp = lll->lll_aux->state;
 
 			/* Further auxiliary PDU reception will be chain PDUs */
 			lll->lll_aux->is_chain_sched = 1U;
+
 		} else {
 			/* Return -ECHILD, as ULL execution has not yet assigned
 			 * an aux context. This can happen only under LLL
diff --git a/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_sync.c b/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_sync.c
index 63b6e9a53b5..f74b5fa145d 100644
--- a/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_sync.c
+++ b/subsys/bluetooth/controller/ll_sw/nordic/lll/lll_sync.c
@@ -805,6 +805,11 @@ static int isr_rx(struct lll_sync *lll, uint8_t node_type, uint8_t crc_ok,
 		 * again a node_rx for periodic report incomplete.
 		 */
 		if (node_type != NODE_RX_TYPE_EXT_AUX_REPORT) {
+			/* Reset Sync context association with any Aux context
+			 * as a new chain is being setup for reception here.
+			 */
+			lll->lll_aux = NULL;
+
 			node_rx = ull_pdu_rx_alloc_peek(4);
 		} else {
 			node_rx = ull_pdu_rx_alloc_peek(3);
diff --git a/subsys/bluetooth/controller/ll_sw/ull_scan_aux.c b/subsys/bluetooth/controller/ll_sw/ull_scan_aux.c
index 4b609017524..17aa91f07bf 100644
--- a/subsys/bluetooth/controller/ll_sw/ull_scan_aux.c
+++ b/subsys/bluetooth/controller/ll_sw/ull_scan_aux.c
@@ -645,6 +645,9 @@ void ull_scan_aux_setup(memq_link_t *link, struct node_rx_pdu *rx)
 	 */
 	if (ftr->aux_lll_sched) {
 		if (IS_ENABLED(CONFIG_BT_CTLR_SYNC_PERIODIC) && sync_lll) {
+			/* Associate Sync context with the Aux context so that
+			 * it can continue reception in LLL scheduling.
+			 */
 			sync_lll->lll_aux = lll_aux;
 
 			/* AUX_ADV_IND/AUX_CHAIN_IND PDU reception is being
@@ -661,8 +664,8 @@ void ull_scan_aux_setup(memq_link_t *link, struct node_rx_pdu *rx)
 			 */
 			LL_ASSERT(!lll->lll_aux || (lll->lll_aux == lll_aux));
 
-			/* scan context get the aux context so that it can
-			 * continue reception in LLL scheduling.
+			/* Associate Scan context with the Aux context so that
+			 * it can continue reception in LLL scheduling.
 			 */
 			lll->lll_aux = lll_aux;
 
@@ -688,11 +691,6 @@ void ull_scan_aux_setup(memq_link_t *link, struct node_rx_pdu *rx)
 		if (unlikely(scan->is_stop)) {
 			goto ull_scan_aux_rx_flush;
 		}
-
-		/* Remove auxiliary context association with scan context so
-		 * that LLL can differentiate it to being ULL scheduling.
-		 */
-		lll->lll_aux = NULL;
 	} else {
 		struct ll_sync_set *sync_set;
 
@@ -705,7 +703,13 @@ void ull_scan_aux_setup(memq_link_t *link, struct node_rx_pdu *rx)
 			goto ull_scan_aux_rx_flush;
 		}
 
-		/* Associate the auxiliary context with sync context */
+		/* Associate the auxiliary context with sync context, we do this
+		 * for ULL scheduling also in constrast to how extended
+		 * advertising only associates when LLL scheduling is used.
+		 * Each Periodic Advertising chain is received by unique sync
+		 * context, hence LLL and ULL scheduling is always associated
+		 * with same unique sync context.
+		 */
 		sync_lll->lll_aux = lll_aux;
 
 		/* Backup the node rx to be dispatch on successfully ULL
@@ -1280,19 +1284,9 @@ static void flush(void *param)
 	scan = HDR_LLL2ULL(lll);
 	scan = ull_scan_is_valid_get(scan);
 	if (!IS_ENABLED(CONFIG_BT_CTLR_SYNC_PERIODIC) || scan) {
-		lll->lll_aux = NULL;
 #if defined(CONFIG_BT_CTLR_JIT_SCHEDULING)
 		lll->scan_aux_score = aux->lll.hdr.score;
 #endif /* CONFIG_BT_CTLR_JIT_SCHEDULING */
-	} else {
-		struct lll_sync *sync_lll;
-		struct ll_sync_set *sync;
-
-		sync_lll = aux->parent;
-		sync = HDR_LLL2ULL(sync_lll);
-
-		LL_ASSERT(sync->is_stop || sync_lll->lll_aux);
-		sync_lll->lll_aux = NULL;
 	}
 
 	aux_release(aux);