Nowadays, consumers demand healthy, safe, and ready-to-eat horticultural products because of their lifestyle. In this regard, new legume-based food product development with eco-innovative technologies seems to be an interesting market. The effect on quality of an innovative pesto sauce, made of fresh faba bean seeds, of an alternative continuous microwave treatment pasteurization (MW, 11 kW; 30 s) regarding a conventional pasteurization (85°C; 5 min) throughout 20 days at 5°C was studied. Non-heated blended samples were used as control. The microbial quality was satisfactory in all treatments. MW treatment improved the sensorial quality of pesto sauce and decreased condensed tannins. Additionally, MW-treated samples showed the best texture, consistency, and color, preserving its chlorophyll and carotenoid content. On the other hand, thermal treatments showed a decrease in total phenolic compounds (TPC) and antioxidant capacity (TEAC) after heating, regarding control samples; however, TPC and TEAC remained quite constant throughout the storage.