Protocols are often viewed or articulated through an instrumental lens – their purpose seen as the means to an end. However, this conception fails to account for the way protocols alter how a participant thinks and acts beyond just giving behavioral direction. Taking a cue from phenomenological methods, which examine objectivity through subjective experience, this essay argues that protocols encourage particular states of being in human participants, and through these states can impair or enhance our ability to pursue human flourishing. Deciding whether to implement a protocol and how to do it becomes, therefore, a moral question – one that is not answerable merely by reference to a protocol’s effectiveness and efficiency in moving towards its immediate goal, but requires taking into account the effect on the individual participant. The hope is that we will design and wield our protocols with greater purpose: as a means to an end and, perhaps, as an end in themselves.