A material deposition system is configured to deposit material on an electronic substrate, such as a printed circuit board. The material deposition system includes a frame, a support coupled to the frame and configured to support an electronic substrate during a deposit operation, a gantry coupled to the frame, and two deposition heads coupled to the gantry. Each deposition head includes a needle, with the deposition heads being movable over the support by movement of the gantry. The material deposition system further includes a needle cleaner assembly movable on a needle cleaner gantry, with the needle cleaner assembly being configured to clean needles of the deposition heads. The material deposition system further includes a controller configured to control the operation of the needle cleaner assembly to perform a needle cleaning operation.