Skeletal muscles are typically considered and modelled as massless and one-dimensional. Yet studies have shown that tissue mass and the three-dimensional (3D) structure of muscle alter contractile behaviour during cyclic contractions; however, it is not yet known how these factors affect the distribution of energy through contracting whole muscle. Therefore, in this study we examined how energy is distributed through muscle tissue during cyclic contractions, and how this is altered by changes in kinetic energy across pennate muscles of different mass. To do this, we simulated cyclic contraction regimes of a three-dimensional finite element model of pennate muscle and varied the size and architecture of the muscle model. We also qualitatively validated the model by comparing its behaviour to that of in situ muscle during analogous experimental trials. We found that greater muscle mass resulted in relatively more mass-specific energy stored as kinetic energy during the simulated contraction cycles, and this was associated with lower mass-specific mechanical work output per cycle. Simulated muscles with higher initial pennation angles showed smaller reductions in mass-specific work with greater muscle mass compared to muscles with lower initial pennations. We additionally found that greater muscle mass and higher cycle strain amplitude led to greater reductions in maximum acceleration near the middle of the muscle tissue compared to at the moving end for both the simulated and experimental contractions. These results show that muscle tissue mass is an important determinant of 3D whole muscle behaviour during cyclic contractions.