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 (≈80%–95%) in shorter reaction times (≈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.