Biochemical energy recovery using digestion and co-digestion of faecal matter collected from urine diverting dehydrating toilet faeces (UDDT-F) and mixed organic market waste (OMW) was studied under laboratory- and pilot-scale conditions. Laboratory-scale biochemical methane potential (BMP) tests showed an increase in methane production with an increase in OMW fraction in the feed substrate. In subsequent pilot-scale experiments, one-stage and two-stage plug flow digester were researched, applying UDDT-F:OMW ratios of 4:1 and 1:0, at about 10 and 12% total solids (TS) slurry concentrations. Comparable methane production was observed in one-stage (Ro-4:1,12%) (314 ± 15 mL CH4/g VS added) and two-stage (Ram-4:1,12%) (325 ± 12 mL CH4/g VS added) digesters, when applying 12% TS slurry concentration. However, biogas production in Ram-4:1,12% digester (571 ± 25 mL CH4/g VS added) was about 12% higher than in Ro-4:1,12%, significantly more than the slight difference in methane production, i.e. 3–4%. The former was attributed to enhanced waste solubilisation and increased CO2 dissolution, resulting from mixing the bicarbonate-rich methanogenic effluent for neutralisation purposes with the low pH (4.9) influent acquired from the pre-acidification stage. Moreover, higher process stability was observed in the first parts of the plug flow two-stage digester, characterised by lower VFA concentrations.