Burning bootloader arduino bootloader on a atsamd21 custom board

Ive just finished designing my custom atsamd21 pcb with a built-in tft touch screen and i need to burn the arduino zero bootloader. Research indicates that not having the embedded debugger chip, i need an atmel ice programmer which is real expensive.

Can anyone point me towards alternative solutions? It would be nice if something equivalent to the arduino-as-isp was avaliable...

Hi @Watcher. I'll share my stock instructions for burning the bootloader to the ATSAMD21G18 boards. I hope you'll forgive that some of the information is not relevant to your specific project.

The TL;DR is that you can use the Adafruit_DAP library to convert a SAMD-based board into a programmer or there are also cheap dedicated debug probe/programmers available (see the last part of the reply).

You'll need:

  • An extra Arduino board that runs at 3.3 V.
  • An SD slot. This could be built into your Arduino board (e.g., MKR Zero), a shield (e.g., MKR SD Proto Shield), or one of the common SD modules.
  • An SD card that fits your SD slot.
  • A way to connect the SD card to your computer.
  • A way to make the connections to the SWD pins on your target Arduino board. For the Nano 33 IoT and the MKR boards other than MKR1000, I like to use a 0.1" pitch 2x3 POGO adapter. You could also solder wires to the test points if you prefer. On the MKR boards other than the MKR1000, the SWD header is on the bottom of the board and is the footprint for a 0.1" pitch 2x3 SMD header (e.g., https://www.digikey.com/short/z3dvdv). On the MKR1000, it is a 0.05" pitch 2x5 male header on the top of the board, which you will need an adapter and cable for.

It is possible to use an Arduino board that runs at 5 V as the programmer, but you'll need to use level shifting circuitry on the programming lines to avoid exposing the target board to 5 V logic levels, which would damage it.


Connect an SD card to your computer.

Open this link in your browser: https://github.com/arduino/ArduinoCore-samd/tree/master/bootloaders

Click the folder that matches the name of your target board.

Click the file that ends in .bin.

Click the "Download" button.

Rename the downloaded file to fw.bin

Move fw.bin to the SD card.

Eject the SD card from your computer.

Plug the USB cable of the Arduino board you will be using as a programmer into your computer.

(In the Arduino IDE) Sketch > Include Library > Manage Libraries

Wait for the download to finish.

In the "Filter your search..." field, type "Adafruit DAP library".

Press "Enter".

Click on "Adafruit DAP library by Adafruit".

Click the "Install" button.

Wait for the installation to finish.

Click the "Close" button.

File > Examples > Adafruit DAP library > flash_from_SD

Change this line:

#define SD_CS 4

according to the Arduino pin connected to the SD CS pin. If your board has a built-in SD slot (e.g., MKR Zero), then you can change this line:

if (!SD.begin(SD_CS)) {


if (!SD.begin()) {

Select the correct board from the Tools > Board menu.

Select the correct port from the Tools > Port menu.

Sketch > Upload

Wait for the upload to finish successfully.

Unplug the programmer Arduino board from your computer.

Plug the SD card into the SD slot connected to your Arduino board.

Connect the programmer Arduino board to the target Arduino board as follows:

| Programmer | | Target | | - | - | | ----------- | |------- | | VCC | | +3V3 | | ----------- | |------- | | 10 | | SWDIO | | ----------- | |------- | | 9 | | SWCLK | | ----------- | |------- | | GND | | GND | | ----------- | |------- | | 11 | | RESETN | | ----------- | |------- |

MKR board (except MKR 1000) SWD pads: |500x348 MKR 1000 SWD header pinout: |500x272 Nano 33 IoT SWD pads: |500x377

Plug the USB cable of the programmer Arduino board into your computer.

Tools > Serial Monitor. You should now see the target board detected, and the bootloader file flashed to it successfully.

Unplug the programmer Arduino board from your computer.

Disconnect the programmer Arduino board from the target Arduino board.

Note: if you have a CMSIS-DAP debugger, you can just do this instead:

  • Connect the debugger to your Arduino board.
  • (In the Arduino IDE) Tools > Programmer > Atmel EDBG
  • Tools > Burn Bootloader

I use this little open source debugger.

Thanks :slight_smile:


Its been some time since my last post on this thread but only now I just collected all components and PCB from China and put everything together.

It seems that something is wrong with my setup. After failing to recognize the target board, I noticed that there is no waveform on the external 32Khz crystal on my board. I would expect a nice sinusoidal waveform there running at the oscillator frequency. Isn't this correct or does the MPU needs to somehow first start the oscillator ?

On AVR boards that I am used to, just powering up a brand new MPU with the necessary decaps starts the oscillator. Is it different for ARM?