The recovery of biomolecules from food industry by-products is of major relevance for a circular economy strategy. However, by-products’ contamination with mycotoxins represents a drawback for their reliable valorization for food and feed, hampering their application range, especially as food ingredients. Mycotoxin contamination occurs even in dried matrices. There is a need for the implantation of monitoring programs, even for by-products used as animal feed, since very high levels can be reached. This systematic review aims to identify the food by-products that have been studied from 2000 until 2022 (22 years) concerning mycotoxins’ contamination, distribution, and prevalence in those by-products. PRISMA (“Preferred Reporting Items for Systematic Reviews and MetaAnalyses”) protocol was performed via two databases (PubMed and SCOPUS) to summarize the research findings. After the screening and selection process, the full texts of eligible articles (32 studies) were evaluated, and data from 16 studies were considered. A total of 6 by-products were assessed concerning mycotoxin content; these include distiller dried grain with solubles, brewer’s spent grain, brewer’s spent yeast, cocoa shell, grape pomace, and sugar beet pulp. Frequent mycotoxins in these by-products are AFB₁, OTA, FBs, DON, and ZEA. The high prevalence of contaminated samples, which surpasses the limits established for human consumption, thus limiting their valorization as ingredients in the food industry. Co-contamination is frequent, which can cause synergistic interactions and amplify their toxicity.