Abstract Reference points are used in fisheries management to infer stock status and inform future fishing opportunities. They can be estimated externally to the assessment model assuming attributes such as stock size to be known without error, or internally where the uncertainty can be accounted for in the estimation. Little is known about the effect of choosing one approach over another on reference point estimates. We compare maximum sustainable yield (MSY) reference points obtained internally in the assessment model (SAM) with those obtained by external estimation (EqSim) via simulations using 11 stocks with known and unknown stock–recruitment relationships (SRRs). Internal estimation of reference points does better on average than external estimation in terms of bias, variance, and SRR selection. Coverage probability of the reference point confidence intervals is good for the internal approach. Stochasticity considerations via re-sampling in the external approach can lead to bias. Bias in reference points have consequences on future yield, stock development, and status. However, it is difficult to predict them by solely looking at bias because they depend on current stock status, recruitment, and extent of bias, but also bias direction since a harvest control rule might compensate for the bias in the future.