We conducted a comparison of the characteristics of dissolved organic matter (DOM) taken from the bio-toilet and other sources. A characterisation of DOM was carried out to assess the stability of the compost generated during the thermophilic and aerobic biodegradation of faeces. In addition, levels of soluble microbial products generated in the bio-toilet composting reactor were compared with those taken from other sources. The results showed that (i) the main component of DOM from the bio-toilet are solutes with molecular weight (MW)>30,000 Da (40%), whereas micromolecules (MW< 1000 Da) constituted more than 60% of the DOM from other solid samples, while liquid samples reached even more than 90%; (ii) the DOM stabilisation level in the composting reactor of the bio-toilet system was greater than that shown by DOM from other sources; (iii) stabilisation of DOM in the bio-toilet system was characterised by an increasing amount of macromolecules (MW>30,000 Da) after a decreasing trend was observed in the early stages of the biodegradation process; and (iv) net production of lipopolysaccharide (LPS) in wastewater treatment plants is greater than in the bio-toilet.