<italic>Chrysomya megacephala</italic> larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions.

Summary: <italic>Chrysomya megacephala</italic> is a saprophagous fly whose larvae can compost manure and yield biomass and bio‐fertilizer simultaneously. However, there are concerns for the safety of the composting system, that is risk of diseases spread by way of manure pathogens, residue of harmful metals and emission of greenhouse gases. Microbiota analysis and heavy metal speciation by European Communities Bureau of Reference were evaluated in raw, <italic>C. megacephala</italic>‐composted and natural stacked swine manure to survey pathogenic bacterial changes and mobility of lead and cadmium in manure after <italic>C. megacephala</italic> feeding; the emission rate of CH4 and N2O from manure during <italic>C. megacephala</italic> composting and natural stacking was also measured. <italic>C. megacephala</italic> composting altered manure microbiota, reduced the risk of pathogenic bacteria and maintained the stability, and microbiota changes might be associated with heavy metal fractions, especially in <italic>Pseudomonas</italic> and <italic>Prevotella</italic>. In addition, <italic>C. megacephala</italic>‐composting significantly reduced the emission rate of CH4 and N2O in comparing with natural stacking situation and the first two days should be the crucial period for CH4 and N2O emission measurement for manure treatment by <italic>C. megacephala</italic>. Moreover, OTU26 and Betaproteobacteria were changed after <italic>C. megacephala</italic> composting which might play a role in emission of CH4 and N2O, respectively. [ABSTRACT FROM AUTHOR]