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The world population and global food demand are increasing, particularly the demand for animal protein sources. At the same time, society produces large quantities of food waste. Sustainable solutions, to ensure enough food and to optimize the use of resources, are necessary. Earthworms grown on fruit and vegetable waste (FVW) can be a future alternative food source, contributing to waste disposal efficiency. They improve food sustainability under nutritional and environmental dimensions. These topics are included in the philosophy of the circular economy. Earthworms, characterized by a high percentage of proteins and minerals, are used as foods in some world countries, including China and the Philippines. In order to consider safety aspects of earthworms grown on FVW as food sources, this study evaluated the microbiological quality of FVW (i) used as growth substrate; fresh earthworms (ii) and earthworms’ meal (iii) resulting from two technological processes (freeze-drying and drying). The efficiency of these technologies in reducing microbial contamination was evaluated. Microbiological analyses revealed the absence of Salmonella spp. and Listeria monocytogenes in FVW, in fresh earthworms and in earthworms’ meal. Fresh earthworms’ results fell within the limits of acceptability, if related to the limit for minced meat (Interdepartmental Center for Research and Documentation on Food Safety). Both freeze-drying and drying step led to a further reduction of microbial contamination, confirming the importance of the processing methods. In conclusion, earthworms can represent an innovative biotechnological response to re-use FVW, a valuable food supplement of animal proteins and a strategy to improve food sustainability.