An all-digital cantilever controller for magnetic resonance force microscopy (MRFM) was developed through a close collaboration between SC Solutions, Cornell University, and the U.S. Army Research Laboratory. The advantage of an all-digital controller is its absence of thermal drift, as well as its great tuning flexibility. This versatile controller is comprised of a Field Programmable Gate Array (FPGA) connected via a low-latency interface to an analog input, an analog output, and a Digital Signal Processor (DSP) with additional analog outputs. Performance of the controller was demonstrated in experiments employing ultra-sensitive silicon microcantilevers fabricated at Cornell University's Nanoscale Science and Technology Facility. The all-digital cantilever controller successfully measured 5 millihertz shins in a 5 Hz detection bandwidth in the resonance frequency of these ultra-sensitive microcantilevers on a millisecond timescale. Independently, a noise floor of 40 microhertz in one second was measured for this controller.