Mojos shipped in 2014 or later have the Arduino compatible bootloader. If your Mojo does not have the Arduino compatible bootloader, we recommend upgrading it. Please visit this page for more instructions.

On the Mojo there is a microcontroller that provides most of the core functionality. As we improve the firmware for the microcontroller by fixing bugs and adding new features, you can update the Mojo by following this tutorial. The microcontroller has a USB bootloader so it is easy to update yourself.

Mojo IDE

If you are using the Alchitry Labs, simply click Tools->Flash Firmware... to flash the latest firmware.

Manual Update

First you will need to download the latest firmware. The latest firmware was posted on March 2, 2016.

The latest update includes some patches to the serial interface to the FPGA which requires you to use the updated Mojo Base Project. These changes ensure no bytes are dropped.

Arduino Compatible Mojo Instructions

The easiest way to update the firmware when an Arduino compatible Mojo is to simply setup the Arduino IDE and grab the latest code from the GIT repository. Instructions for doing this can be found on the Arduino setup page.

However, if you want to just flash the hex without installing the Arduino IDE and applying the modifications, you can use avrdude to program it.


It's really easy to update using Linux. Simply install avrdude by typing the following.

sudo apt-get install avrdude

Then navigate to the folder with the hex file and run avrdude. Before you run avrdude, make sure you get the Mojo in bootloader mode by temporarily shorting the pins shown at the bottom of the page.

avrdude -P /dev/ttyACM0 -c avr109 -p m32u4 -U flash:w:Mojo-v3-Loader-1.2.5.hex

Make sure to change /dev/ttyACM0 to the correct port for the Mojo!

The hex should now be loaded on the Mojo!


Head over to SourceForge and download WinAVR.

After it's installed click Start->Run and type cmd to open a command prompt.

Navigate to where the hex file is and enter the following. Before you run avrdude, make sure you get the Mojo in bootloader mode by temporarily shorting the pins shown at the bottom of the page.

avrdude -P COM4 -c avr109 -p m32u4 -U flash:w:Mojo-v3-Loader-1.2.5.hex

Make sure to change COM4 to the port the Mojo is connected to. Note that this port may change after you put the Mojo is bootloader mode. It will only stay in bootloader mode for about 15-20 seconds and it will show up in the Device Manger as Mojo V3 bootloader. If you miss the bootloader window, simply short the pins again to re-enter it.

The hex should noe be loaded on the Mojo!

Legacy Mojo Instructions


It is pretty easy to update the Mojo in Ubuntu using dfu-programmer.

First you need to install dfu-programmer. Open a terminal and enter

sudo apt-get install dfu-programmer

You also need to download the following file and place it in /etc/udev/rules.d. You will need superuser privileges to do this.

Mojo USB Rules

Once you add the rules file, you will need to unplug and re-plug the Mojo to have it take effect.

Jump down to Entering Bootloader Mode for instructions on how to get the Mojo into bootloader mode.

You can now update the Mojo with the following commands.

dfu-programmer atmega32u4 erasedfu-programmer atmega32u4 flash /path/to/hex/file/Mojo-Loader-1.2.5.hexdfu-programmer atmega32u4 start

Note that if you have a Mojo V2 the board probably has an ATmega16U4 microcontroller and not an ATmega32U4. In that case, replace atmega32u4 with atmega16u4 in the above commands.

The firmware is now updated.


To update the Mojo in Windows you will need to download FLIP.

FLIP Download Page

There are two flavors of FLIP, one with a Java Runtime included and one without. Either will work as long as you have Java installed on your computer. If you are unsure if you have Java or not, download the one with the Runtime included.

Once you've installed FLIP, jump down to Entering Bootloader Mode for instructions on how to get the Mojo into bootloader mode.

Windows may or may not find the driver for your Mojo. If it doesn't, open the Device Manager. It should look similar to below.


Right click on the ATm32U4DFU or ATm16U4DFU, depending on your Mojo, and click Update Driver Software...

Then choose Browse my computer for driver software and fill in the path to where you installed FLIP. Select the sub-folder usb.


Click Next and install the driver.

Once the driver is installed, launch FLIP.

Click on the chip icon in the upper left corner and choose the microcontroller your Mojo has. If you have a Mojo V2 chances are you have an ATmega16U4, although some have ATmega32U4's. If you have a Mojo V3 you have an ATmega32U4.

Click on the icon of the USB cable and choose USB then Open.

Next, click on the red book that has the red arrow pointing into it. When you hover over it with your mouse it should say Load HEX File. Select the Mojo-Loader-1.2.hex file you downloaded.


Finally click on Run. Once that finishes click Start Application. The firmware is now updated!

Entering Bootloader Mode

To program the microcontroller you need to get it into bootloader mode.

First plug the Mojo into your computer. With the Mojo still powered on, flip it over so you see the six little pads above the last O in Mojo. You need to momentarily connect the two leftmost pads. A jumper wire works well for this. Connecting these pads resets the microcontroller and on restart it will enter the bootloader.

The image below shows the pins to connect.


Once you tap those together it should be in bootloader mode. Jump back to your operating system's section.