Cognitive control is critical for accomplishing daily tasks and yet we experience it as effortful or costly. Researchers have been increasingly interested in estimating how costly cognitive control is for a given individual, to better understand underlying mechanisms and predict motivational impairments outside the lab. Here we leverage a computational model of control allocation to (a) demonstrate a procedure for estimating individual's control costs from task performance and (b) highlight the conditions under which estimated costs will be confounded with other motivational variables. We show that costs of cognitive control can be reliably estimated under perfect assumptions about other motivational variables. However, our simulation results indicate that poorly calibrated estimates of those other variables can lead to potentially drastic misestimations of subjects' control costs, compromising the validity of empirical observations. We conclude by discussing the implications of these analyses for assessing individual differences in the costs of cognitive control.