Industrial hazardous-waste regulations seldom fit academic laboratories, where small batches, diverse chemicals, and rotating users prevail; prior studies apply ISO 14001, LCA, Lean and Six Sigma mostly in industry. This work addresses urgent compliance and safety gaps in a Peruvian university’s laboratories. We integrate ISO 14001, LCA principles, Green Lean, and Green Six Sigma within a DMAIC framework, using E-VSM, cradle-to-grave tracking, digitalized forms, and targeted training. Audited results show compliance rising from 22% to 61% (Industrial Engineering) and 18% to 78% (Civil Engineering), average storage time falling from 15 to 6 and <1 month, and traceability and training coverage increasing from 0–53%/10% to >90%. Academically, the study adapts industrial-quality tools to high-variability academic settings; socioeconomically, it reduces risk and strengthens institutional governance. We invite researchers to test the model across faculties and quantify environmental impacts with full LCA.