The free energy principle, an influential framework in computational neuroscience and theoretical neurobiology, starts from the assumption that living systems ensure adaptive exchanges with their environment by minimizing the objective function of variational free energy. Following this premise, it claims to deliver a promising integration of the life sciences. In recent work, Markov blankets, one of the central constructs of the free energy principle, have been applied to resolve debates central to philosophy (such as demarcating the boundaries of the mind). The aim of this paper is twofold. First, we trace the development of Markov blankets starting from their standard application in Bayesian networks, via variational inference, to their use in the literature on active inference. We then identify a persistent confusion in the literature between the formal use of Markov blankets as an epistemic tool for Bayesian inference, and their novel metaphysical use in the free energy framework to demarcate the physical boundary between an agent and its environment. Consequently, we propose to distinguish between “Pearl blankets” to refer to the original epistemic use of Markov blankets and “Friston blankets” to refer to the new metaphysical construct. Second, we use this distinction to critically assess claims resting on the application of Markov blankets to philosophical problems. We suggest that this literature would do well in differentiating between two different research programmes: “inference with a model” and “inference within a model.” Only the latter is capable of doing metaphysical work with Markov blankets, but requires additional philosophical premises and cannot be justified by an appeal to the success of the mathematical framework alone.