The study aims to investigate the effects of different loads and speed during running on inter- and intra-individual muscle force amplitudes, variabilities and coordination patterns. Nine healthy participants ran on an instrumentalized treadmill with an empty weight vest at two velocities (2.6 m/s and 3.3 m/s) or while carrying three different loads (4.5, 9.1, 13.6 kg) at 2.6 m/s while kinematics and kinetics were synchronously recorded. The major lower limb muscle forces were estimated using a musculoskeletal model. Muscle force amplitudes and variability, as well as coordination patterns were compared at the group and at the individual level using respectively statistical parametric mapping and covariance matrices combined with multidimensional scaling. Increasing the speed or the load during running increased most of the muscle force amplitudes (p < 0.01). During the propulsion phase, increasing the load increased muscle force variabilities around the ankle joint (modification of standard deviation up to 5% of body weight (BW), p < 0.05) while increasing the speed decreased variability for almost all the muscle forces (up to 10% of BW, p < 0.05). Each runner has a specific muscle force coordination pattern signature regardless of the different experimental conditions (p < 0.05). Yet, this individual pattern was slightly adapted in response to a change of speed or load (p < 0.05). Our results suggest that adding load increases the amplitude and variability of muscle force, but an increase in running speed decreases the variability. These findings may help improve the design of military or trail running training programs and injury rehabilitation by progressively increasing the mechanical load on anatomical structures.