In this work, we report an effective, one-pot syntheses of benzo[4,5]imidazo[1,2-a]pyrimidine and pyrano[4,3-b]pyran derivatives using L-glutamine functionalized nanoparticles (Fe3O4@SiO2@L-glutamine NPs) under microwave irradiation. The organo-nanocatalyst underwent characterization through diverse techniques, including FT-IR, p-XRD, SEM, TEM, EDX, XPS, TGA, and VSM. Microwave irradiation and multicomponent reactions synergistically yield excellent product yields (approximate to 80%-95%) in shorter reaction times (approximate to 6-15 min) with a broader substrate scope. The organo-nanocatalyst displays notable catalytic efficacy, evidenced by high turnover numbers (TON) and turnover frequencies (TOF) across syntheses. This innovative protocol showcases exceptional efficiency, cost-effectiveness, and environmental friendliness, with advantages like minimal reaction conditions, easy catalytic recovery, recyclability, operational simplicity, and the use of eco-friendly solvents.