Physiological assessment of soccer training usually refers to the measurement of anatomical, physiological, biochemical and functional changes specific to the sport discipline (training outcome). The quality, quantity and organization of physical exercises (training process) are, on the other hand, usually described by the external work imposed by the coach on his or her athletes. In this review, we demonstrate that this approach is not appropriate in soccer, as training is often based on group exercises. The physiological stress (internal load) induced by such training often differs between individuals. Here, we present some physiological laboratory-based tests and field tests used to evaluate training outcomes in soccer, together with methods based on heart rate and perceived exertion to quantify internal load imposed during training. The integrated physiological assessment of both training outcome and process allows researchers: (1) to improve interpretation of physical tests used to verify the effectiveness of training programmes; (2) to evaluate the organization of the training load in order to design periodization strategies; (3) to identify athletes who are poor responders; (4) to control the compliance of the training completed to that planned by the coach; and (5) to modify the training process before the assessment of its outcome, thus optimizing soccer performance.