Asbtract Stock–recruitment relationships (SRRs) may vary over time due to ecological and anthropogenic impacts, challenging traditional approaches of calculating maximum sustainable yield (MSY)-based reference points that assume constant population traits. We compare seven methods to calculate MSY, FMSY and BMSY by modelling constant, stochastic (uncorrelated), and autocorrelated SRRs using simulations and two case studies [Atlantic cod (Gadus morhua) and American plaice (Hippoglossoides platessoides) on the Grand Bank off Newfoundland, Canada]. Results indicated that the method used to model SRRs strongly affected the temporal pattern of recruitment projection, and the variations generated by autocorrelated SRRs were more similar to observed patterns. When the population productivity had low-frequency and large-magnitude variations, stochastic SRRs generated greater MSY and FMSY estimates than constant or autocorrelated SRRs, while no consistent pattern of BMSY was detected. In the case studies, stochastic and autocorrelated SRRs produced asymmetric relationships between fishing mortality and yield, with higher risk of overfishing by going beyond FMSY. Overall, our results suggest that caution should be taken when calculating MSY-based reference points in highly dynamic ecosystems, and correctly accounting for non-stationary population dynamics could, therefore, lead to more sustainable fisheries.