The evolution of phosphine gas during the anaerobic batch fermentation of fresh swine manure was detected and correlated to the production of methane and hydrogen sulphide. A close temporal relationship between phosphine liberation and methane formation was found. However, the gaseous phosphine released from manure during fermentation only represents a tiny fraction of the overall phosphine balance. The majority of phosphine is captured in solid manure constituents. This matrix‐bound phosphine is eliminated by more than 50% during anaerobic batch‐fermentation. Seasonally determined phosphine concentrations in biogas and manure from two large‐scale manure treatment plants also revealed net losses of phosphine in fermentation. Consequently, manure has to be considered more as a sink of phosphine rather than a phosphine‐generating medium. Furthermore, a close relationship between phosphine in the feed of swine and manure of these swine was observed, implying that phosphine residues in the feed (possibly as a result of grain fumigation) represent an important source of phosphine in manure technologies that is relevant before the faecals of swine enter manure treatment plants.