Fault detection in microgrids presents a strong technical challenge due to the dynamic operating conditions. Changing the power generation and load impacts the current magnitude and direction, which has an adverse effect on the microgrid protection scheme. To address this problem, this paper addresses a field-transform-based fault detection method immune to the microgrid conditions. The faults are simulated via a Matlab/Simulink model of the grid-connected photovoltaics-based DC microgrid with battery energy storage. Short-time Fourier transform is applied to the fault time signal to obtain a frequency spectrum. Selected spectrum features are then provided to a number of intelligent classifiers. The classifiers’ scores were evaluated using the F1-score metric. Most classifiers proved to be reliable as their performance score was above 90%.