Green chemistry and chemical safety complement each other in reducing adverse health and safety outcomes. However, it is imperative to train students of advanced synthetic chemistry, beyond reaction mechanisms, to proactively connect complex experiments with hazard analysis, risk minimization, and planetary sustainability. Virtual experiments provide an opportunity for students to critically reinvent the way organic synthetic chemistry is practiced and become stakeholders in designing their own green chemistry experiments. We present a novel project-based learning (PBL) experience where students designed their own, multistep, green chemistry experiment using the virtual platform Beyond Labz, supported with primary literature. The designed experiments capitalized on the safe, energy, and resource nonintensive nature of the virtual platform to inspect chemical variations that would traditionally be hazardous or inaccessible within a physical undergraduate laboratory. Students worked collaboratively in guided groups to synthesize a designated product, combining literature-based procedures and structural analysis through thin layer chromatography (TLC), Fourier transform infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopies. They estimated reagent amounts, calculated atom economy, E-factor, and the process mass intensity of the reactions, and used safety data sheets to assess the inherent hazards of the reactions to recommend modifications, substitutions, or greener alternatives. Students also developed critical scientific communication skills by presenting their designed green experiments in a virtual presentation and individual technical reports. Student survey data indicated that designing their own green synthetic experiments was effective in cultivating a keen awareness of laboratory safety, chemical waste and their impacts and also in inspiring students to become stakeholders in sustainable chemical design and decision making.