Virtual reality (VR) educational games are growing in demand, partly because of evidence found of the benefit of using embodied gestures in educational VR games. Little research has investigated how presence, which is the subjective experience of existing in a virtual world, impacts player learning gains when playing an embodied STEM VR games. The current study investigates how presence impacts learning gains in four conditions. This study evaluated 122 participants’ subjective experiences of presence via an experimenter-designed Presence Scale after playing an educational STEM VR game. ANOVAs were conducted to evaluate differences in learning gains by condition and to also ascertain how presence was affected by cognitive load. Results revealed that presence did not impact learning gains, although high embodiment and high immersion significantly predicted presence. These findings contribute to understanding the effects of embodiment on VR educational games, and how to design for VR user-ability.