Proton beam therapy has been proven to be effective for cancer treatment. Protons allow for complete energy deposition to occur inside patients, rendering this a superior treatment compared to other types of radiotherapy based on photons or electrons. This same characteristic makes quality assurance critical driving the need for detectors capable of direct beam positioning and fluence measurement. This work showcases a flexible and scalable data acquisition system for a multi-channel and segmented readout parallel plate ionization chamber instrument for proton beam fluence and positioning detection. Utilizing readily available, modern, off-the-shelf hardware components, including an FPGA with an embedded CPU in the same package, a data acquisition system for the detector was designed. The undemanding detector signal bandwidth allows the absence of ASICs and their associated costs and lead times in the system. The data acquisition system is showcased experimentally for a 96-readout channel detector demonstrating sub millisecond beam characteristics and beam reconstruction. The system demonstrated scalability up to 1064-readout channels, the limiting factor being FPGA I/O availability as well as amplification and sampling power consumption.