The role of intramuscular metabolite changes in the adaptations following isometric strength training was examined by comparing the effect of short, intermittent contractions (IC) and longer, continuous (CC) contractions. In a parallel study, the changes in phosphate metabolites and pH were examined during the two protocols using whole-body nuclear magnetic resonance spectroscopy (NMRS). Seven subjects trained three time per week for 14 weeks. The right leg was trained using four sets of ten contractions, each lasting 3 s with a 2-s rest period between each contraction and 2 min between each set. The left leg was trained using four 30-s contractions with a 1-min rest period between each. Both protocols involved isometric contractions at 70% of a maximum voluntary isometric contraction (MVC). The MVC, length:tension and force:velocity relationships and cross-sectional area (CSA) of each leg were measured before and after training. The increase in isometric strength was significantly greater (P = 0.041) for the CC leg (median 54.7%; P = 0.022) than for IC (31.5%; P = 0.022). There were no significant differences between the two protocols for changes in the length:tension or force:velocity relationships. There were significant increases in muscle CSA for the CC leg only. NMRS demonstrated that the changes in phosphate metabolites and pH were greater for the CC protocol. These findings suggest that factors related to the greater metabolite changes during CC training results in greater increases in isometric strength and muscle CSA.