The study evaluates Hermetia illucens larvae’s ability to decrease direct methane emissions and nutrients from cattle and swine manure. Hermetia illucens larvae were put into fresh cattle and swine manure, and the same conditions, without larvae, for the control treatment were established. The methane emissions were measured until the first prepupae appeared. The methane emissions from the bioconversion of animal manure by Hermetia illucens larvae were up to 86% lower than in the control treatments (conventional storage). The cumulative methane emissions from cattle and swine manure bioconversion were 41.4 ± 10.5 mg CH4 kg−1 and 134.2 ± 17.3 mg CH4 kg−1, respectively. Moreover, Hermetia illucens larvae could reduce 32% of dry matter, 53% nitrogen, 14% phosphorus, and 42% carbon in swine manure. Meanwhile, in cattle manure, reductions of 17% of dry matter, 5% of nitrogen, 11% of phosphorus, and 15% of carbon and pH reductions in both swine and cattle manure were found. Thus, the production of larvae was higher in swine manure than cattle manure. Furthermore, the larvae frass from swine manure was appropriate for agricultural use, unlike the larvae frass from cattle manure requiring further processing. These results reveal the ability of Hermetia illucens larvae to mitigate methane emissions from animal manure and show it to be a promising technology for manure treatment, with great potential to promote a circular economy in the livestock sector. Graphical abstract: [Figure not available: see fulltext.].