A system for controlling an integrated pump and energy recovery system is disclosed. The processor-based device is configured to receive a position signal representative of a measured position of a piston assembly movable between a top dead center and a bottom dead center of a hydraulic cylinder and a pumping cylinder, from the position sensor. The processor-based device is also configured to receive a pressure signal representative of a measured pressure of at least one of a fluid medium fed from the pumping cylinder to a filtering device, a hydraulic fluid fed from the hydraulic pump to the hydraulic cylinder, from the pressure sensing unit. The processor-based device is further configured to generate a control signal based on the position signal and the pressure signal, and transmit the control signal to the hydraulic power unit to control measured position of the piston assembly and a pressure of the fluid medium.