The AVR is programmed in the ANSI specification of the C programming language. The software is enhanced with device specific functions that allow use of specialized hardware as well as the input and output information of certain pins. The software can be written in any program (including notepad), but to compile the program a version of gcc (C compiler) that can compile the code must be used to create the necessary hex code. The AVR Crosspack for for windows and Mac OS X will install all of the necessary software by default. Once the C code has been compiled its written to the microcontroller through use of the avrdude program which is also installed with the Crosspack.

The AVR is capable of inline serial programming via SPI which means it can be programmedwhile on a circuitboard or breadboard. The programmed was done through the use of adafruit's usbtiny isp programmer: a simple and inexpensive programmer.

To program the microcontroller, you have to execute the following commands within the project directory:

make clean
make all
make load

If the programmer is configured correctly in the makefile (and hooked up correctly) and the program doesn't elicit any errors, the program will be written to the device.