The rapid perishability of microgreens poses a significant challenge to their commercialization, despite their high nutritional value and health benefits. This study addresses the need for effective preservation strategies to extend the shelf-life of arugula (Eruca sativa Mill.) microgreens, a particularly perishable product. The objective was to evaluate the impact of different packaging methods on maintaining the sensory, biochemical, and physiological attributes of arugula microgreens during refrigerated storage. Arugula microgreens were grown under controlled conditions. They were then packaged in non-perforated polypropylene bags (PB) or micro-perforated polypropylene bags (MPB), and compared to unpackaged samples (NP) under simulated supermarket conditions (10 °C with alternating 12-hour light/dark cycles). Shelf-life was assessed through sensory evaluation (visual and olfactory quality), headspace gas composition, chlorophyll content, antiradical activity, total phenolic compounds, and carotenoid profiles. Microgreens in MPB exhibited the best preservation, maintaining visual quality and minimizing off-odors for up to 14 days. Unpackaged samples deteriorated within seven days, and those in PB experienced excessive moisture accumulation. MPB packaging also maintained stable oxygen levels and prevented excessive carbon dioxide accumulation. MPB-stored microgreens retained higher chlorophyll and carotenoid content, with only a 15% reduction in chlorophyll after 14 days, indicating slower degradation. MPB bags are superior for preserving the quality and extending the shelf-life of arugula microgreens, offering practical benefits for the fresh produce industry by reducing waste and enhancing nutritional value.