In comparative experiments with Ca2+ ATPase in native sarcoplasmic reticulum vesicles and reconstituted proteoliposomes, we find that a variable stoichiometry of Ca2+ or Sr2+ transport per ATPase cycle is observed in the absence of passive leak through independent channels. The observed ratio is commonly lower than the optimal value of 2 and depends on the composition of the reaction mixture. In all cases, a progressive rise in the lumenal concentration of Ca2+ and Sr2+ is accompanied by a parallel reduction of coupling ratios. Significant ATPase activity remains even after asymptotic levels of Ca2+ accumulation are reached. This residual activity subsides if the Ca2+ concentration in the outer medium is reduced below activating levels (as it would following Ca2+ transients in muscle fibers). The reduction of stoichiometric coupling is explained with a reaction scheme, including a branched pathway for hydrolytic cleavage of phosphorylated intermediate before release of Ca2+ into the lumen of the vesicles. Flux through this pathway is favored when net lumenal Ca2+ dissociation from the phosphoenzyme is impeded and results in P(i) production accompanied by lumenal and medium Ca2+ exchange. Occurrence of reactions through branched pathways may have general implications for the stoichiometric efficiency of energy-transducing enzymes.