diff --git a/ports/atmel-samd/mpconfigport.mk b/ports/atmel-samd/mpconfigport.mk
index af33edb0eb..dfc8d3abb7 100644
--- a/ports/atmel-samd/mpconfigport.mk
+++ b/ports/atmel-samd/mpconfigport.mk
@@ -19,6 +19,9 @@ ifeq ($(CHIP_FAMILY),samd21)
 # frequencyio not yet verified as working on SAMD21.
 CIRCUITPY_FREQUENCYIO = 0
 CIRCUITPY_TOUCHIO_USE_NATIVE = 1
+
+# SAMD21 needs separate endpoint pairs for MSC BULK IN and BULK OUT, otherwise it's erratic.
+USB_MSC_NUM_ENDPOINT_PAIRS = 2
 endif
 
 # Put samd51-only choices here.
diff --git a/supervisor/supervisor.mk b/supervisor/supervisor.mk
index 016188dfd9..e758ea2165 100644
--- a/supervisor/supervisor.mk
+++ b/supervisor/supervisor.mk
@@ -89,6 +89,11 @@ ifndef USB_HID_DEVICES
 USB_HID_DEVICES = "KEYBOARD,MOUSE,CONSUMER,GAMEPAD"
 endif
 
+# SAMD21 needs separate endpoint pairs for MSC BULK IN and BULK OUT, otherwise it's erratic.
+ifndef USB_MSC_NUM_ENDPOINT_PAIRS
+USB_MSC_NUM_ENDPOINT_PAIRS = 1
+endif
+
 SUPERVISOR_O = $(addprefix $(BUILD)/, $(SRC_SUPERVISOR:.c=.o)) $(BUILD)/autogen_display_resources.o
 
 $(BUILD)/supervisor/shared/translate.o: $(HEADER_BUILD)/qstrdefs.generated.h
@@ -106,8 +111,9 @@ autogen_usb_descriptor.intermediate: ../../tools/gen_usb_descriptor.py Makefile
 		--vid $(USB_VID)\
 		--pid $(USB_PID)\
 		--serial_number_length $(USB_SERIAL_NUMBER_LENGTH)\
-	        --devices $(USB_DEVICES) \
-		--hid_devices $(USB_HID_DEVICES) \
+	        --devices $(USB_DEVICES)\
+		--hid_devices $(USB_HID_DEVICES)\
+		--msc_num_endpoint_pairs $(USB_MSC_NUM_ENDPOINT_PAIRS)\
 		--output_c_file $(BUILD)/autogen_usb_descriptor.c\
 		--output_h_file $(BUILD)/genhdr/autogen_usb_descriptor.h
 
diff --git a/tools/gen_usb_descriptor.py b/tools/gen_usb_descriptor.py
index 82d2daf0f7..87219194bc 100644
--- a/tools/gen_usb_descriptor.py
+++ b/tools/gen_usb_descriptor.py
@@ -32,6 +32,8 @@ parser.add_argument('--devices', type=lambda l: tuple(l.split(',')), default=DEF
                     help='devices to include in descriptor (AUDIO includes MIDI support)')
 parser.add_argument('--hid_devices', type=lambda l: tuple(l.split(',')), default=DEFAULT_HID_DEVICES,
                     help='HID devices to include in HID report descriptor')
+parser.add_argument('--msc_num_endpoint_pairs', type=int, default=1,
+                    help='Use 1 or 2 endpoint pairs for MSC (1 bidirectional, or 1 input + 1 output (required by SAMD21))')
 parser.add_argument('--output_c_file', type=argparse.FileType('w'), required=True)
 parser.add_argument('--output_h_file', type=argparse.FileType('w'), required=True)
 
@@ -45,6 +47,9 @@ unknown_hid_devices = list(frozenset(args.hid_devices) - ALL_HID_DEVICES_SET)
 if unknown_hid_devices:
     raise ValueError("Unknown HID devices(s)", unknown_hid_devices)
 
+if args.msc_num_endpoint_pairs not in (1, 2):
+    raise ValueError("--msc_num_endpoint_pairs must be 1 or 2")
+
 
 class StringIndex:
     """Assign a monotonically increasing index to each unique string. Start with 0."""
@@ -153,7 +158,9 @@ msc_interfaces = [
                 bInterval=0),
             standard.EndpointDescriptor(
                 description="MSC out",
-                bEndpointAddress=0x1 | standard.EndpointDescriptor.DIRECTION_OUT,
+                # SAMD21 needs to use a separate pair of endpoints for MSC.
+                bEndpointAddress=((0x1 if args.msc_num_endpoint_pairs == 2 else 0x0) |
+                                  standard.EndpointDescriptor.DIRECTION_OUT),
                 bmAttributes=standard.EndpointDescriptor.TYPE_BULK,
                 bInterval=0)
         ]