Systems and methods for non-intrusive closed-loop control of internal combustion engines are provided. Systems of the non-intrusive closed-loop control of internal combustion engines include a plurality of engine operating condition sensors, an electronic control unit with a Gaussian process model, and a look-up table. The electronic control unit estimates an MFB50 of the internal combustion engine using the Gaussian process model and with engine operating condition data as input. A desired MFB50 is obtained from the look-up table and a command of a control parameter to a fuel injector for the internal combustion engine is executed by the electronic control unit and as a function of the comparison of the estimated MFB50 and the desired MFB50.