In this 2 × 2 between-subject experimental study, a virtual reality (VR) laboratory simulation is paired with a VR molecular world intervention to teach chemistry concepts. The independent variables are the implementation timing of the molecular world intervention (Pre-lab vs. Integrated) and the level of embodiment (Traditional vs. VR). Eighty students (N = 80), ages 11–18 years old, from a community center in New York City participated, completing a pretest, a laboratory simulation, a molecular intervention, and a post-test. The pre- and post-test measures included multiple-choice, free-response, and drawing questions. A key finding was that integrating the intervention within the lab simulation, no matter which level of embodiment, led to significantly higher gains in learning. The combination of using physical manipulatives and integrating them within the lab exercise (Integrated Traditional condition) demonstrated the greatest gains overall. On drawing measures, the Integrated VR condition showed significant improvement in three out of the four drawing categories (i.e., molecule shape, atom quantity, and relative sizes). The implications are that even though using a VR molecular world intervention can lead to significant learning of abstract chemistry content, the use of physical manipulatives is still a more effective tool.