We present the optimization method for the electron multiplying charge coupled devices of the acquisition system of the SPARC4 (OMASS4). The OMASS4 uses as figures of merit the signal-to-noise ratio (SNR) and the acquisition rate (AR) as a function of the operation mode of the CCDs. Three different modes of optimization are included in the OMASS4: (1) optimization of SNR only; (2) optimization of AR only; and (3) optimization of both SNR and AR simultaneously. The first two modes calculate an analytical maximization of the cost function, whereas the third mode uses the Bayesian optimization method to determine the optimum mode of operation. We apply the OMASS4 to find the optimum mode for observations obtained at the Pico dos Dias Observatory, Brazil and compare the delivered modes of operation and its performance with the ones adopted by the observer. If the OMASS4 had been used as a tool to optimize the CCDs in all of these nights, it would be possible to improve their efficiency in 97.17%, 65.08%, and 77.66% for the optimization modes 1, 2, and 3, respectively.