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Mesquite fruits Prosopis spp. are an important food resource for both humans and animals due to their high nutritional value, but key dietary components are unevenly distributed within the fruit. While carbohydrates occur in the soft, outer mesocarpo, proteins are found in the much harder seeds. This raises the potential for differences in processing costs, and may explain variation in the use of mesquite seeds described ethnographically. Here we report the results of a series of processing experiments that evaluate the nutritional value and time costs associated with increasing levels of mesquite processing (gathering and grounding) using traditional manos and metates. We show that while additional processing does lead to more protein in mesquite flour as seeds are broken down, differences in nutritional value are minimal, overall energetic value remains the same, and the high additional processing costs reduce energetic return rates. These results suggest that under most circumstances mesquite processed using these technologies would be done mostly to extract the carbohydrates. A comparison of residual plant parts from these experiments with similar plant macrofossils from regional archaeological sites suggest similar patterns of processing in the past, with an anthropogenic rather than natural origin for the recovered remains.