Exposure to mycotoxins is a worldwide concern as their occurrence is unavoidable and varies among geographical regions. Mycotoxins can affect the performance and quality of livestock production and act as carriers putting human health at risk. Feed can be contaminated by various fungal species, and mycotoxins co-occurrence, and modified and emerging mycotoxins are at the centre of modern mycotoxin research. Preventing mould and mycotoxin contamination is almost impossible; it is necessary for producers to implement a comprehensive mycotoxin management program to moderate these risks along the animal feed supply chain in an HACCP perspective. The objective of this paper is to suggest an innovative integrated system for handling mycotoxins in the feed chain, with an emphasis on novel strategies for mycotoxin control. Specific and selected technologies, such as nanotechnologies, and management protocols are reported as promising and sustainable options for implementing mycotoxins control, prevention, and management. Further research should be concentrated on methods to determine multi-contaminated samples, and emerging and modified mycotoxins.