Human excrement composting (HEC) is a sustainable strategy for human excrement (HE) management that recycles nutrients and mitigates health risks while reducing reliance on freshwater, fossil fuels, and fertilizers. We present a comprehensive microbial time series analysis of HEC and show that the initial gut-like microbiome of HEC systems transitions to a microbiome similar to soil and traditional compost in fifteen biological replicates tracked weekly for one year.