We examined the relationship amongst baseline work rate (WR), phase II pulmonary oxygen uptake (V̇(O2p)) time constant (τV̇(O2p)) and functional gain (G(P)=ΔV̇(O2p)/ΔWR) during moderate-intensity exercise. Transitions were initiated from a constant or variable baseline WR. A validated circulatory model was used to examine the role of heterogeneity in muscle metabolism (V̇(O2m)) and blood flow (Q̇(m)) in determining V̇(O2p) kinetics. We hypothesized that τV̇(O2p) and G(P) would be invariant in the constant baseline condition but would increase linearly with increased baseline WR. Fourteen men completed three to five repetitions of ∆40 W step transitions initiated from 20, 40, 60, 80, 100 and 120 W on a cycle ergometer. The ∆40 W step transitions from 60, 80, 100 and 120 W were preceded by 6 min of 20 W cycling, from which the progressive ΔWR transitions (constant baseline condition) were examined. The V̇(O2p) was measured breath by breath using mass spectrometry and a volume turbine. For a given ΔWR, both τV̇(O2p) (22-35 s) and G(P) (8.7-10.5 ml min(-1) W(-1)) increased (P < 0.05) linearly as a function of baseline WR (20-120 W). The τV̇(O2p) was invariant (P < 0.05) in transitions initiated from 20 W, but G(P) increased with ΔWR (P < 0.05). Modelling the summed influence of multiple muscle compartments revealed that τV̇(O2p) could appear fast (24 s), and similar to in vivo measurements (22 ± 6 s), despite being derived from τV̇(O2p) values with a range of 15-40 s and τQ̇(m) with a range of 20-45 s, suggesting that within the moderate-intensity domain phase II V̇(O2p) kinetics are slowed dependent on the pretransition WR and are strongly influenced by muscle metabolic and circulatory heterogeneity.