The first Life-Cycle Assessment (LCA) of an acid-free, microwave-assisted process for pectin production at pilot scale is reported. The properties of the resulting pectin were measured and compared against the criteria for commercial pectin, while the energy consumption of the microwave process was measured to compare its life cycle impacts with that of the current commercial process. Overall, the pectin met all the criteria for food-grade commercial pectin. The microwave unit was estimated to have <25% of the environmental impact of traditional acid-assisted thermal process in all categories measured and provided an improved yield of 5% (wet weight basis) compared to 3% by thermal heating under normalized conditions. The readouts were comparable with each other over three runs indicating a robust and reproducible process, crucial for scale-up purposes. With the product meeting the relevant criteria and the process being robust and more environmentally friendly, this work demonstrates the practical and commercial potential of microwave technology to succeed conventional acid-based extraction of pectin production.