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Abstract Fisheries are often characterized by high heterogeneity in the spatial distribution of habitat quality, as well as fishing effort. However, in several fisheries, the objective of achieving a sustainable yield is addressed by limiting Total Allowable Catch (TAC), set as a fraction of the overall population, regardless of the population's spatial distribution and of fishing effort. Here, we use an integral projection model to investigate how stock abundance and catch in the green abalone fishery in Isla Natividad, Mexico, are affected by the interaction of heterogeneity in habitat quality and fishing effort, and whether these interactions change with Allee effects—reproductive failure in a low-density population. We found that high-quality areas are under-exploited when fishing pressure is homogeneous but habitat is heterogeneous. However, this leads to different fishery outcomes depending on the stock's exploitation status, namely: sub-optimal exploitation when the TAC is set to maximum sustainable yield, and stability against collapses when the fishery is overexploited. Concentration of fishing effort in productive areas can compensate for this effect, which, similarly, has opposite consequences in both scenarios: fishery performance increases if the TAC is sustainable but decreases in overexploited fisheries. These results only hold when Allee effects are included.