High-carbon industrial wastewaters are attractive for anaerobic biological waste-to-energy treatment approaches. However, some waste streams, such as those from the personal care product industry (PCP), also can contain inhibitory compounds that impair biogas production (methane; CH4), reducing potential energy recovery. Here we show how source separation of PCP wastes can increase gross CH4 production by shunting inhibitory streams around the methanogenic treatment step. Methane production was compared between shampoo and hair colorant liquid wastes as sources for waste-to-energy applications. Methane yields were five times greater for comparable COD shampoo versus colorant wastes in batch reactors (~250 versus ~50ml CH4/mg COD), suggesting colorant waste constituents impair methanogenesis, although anaerobic treatment reduced the toxicity of both wastes (i.e., Daphnia magna IC50 tolerance values increased from 0.23±0.07 and 0.17±0.04%v/v to 38.0±2.0 and 15.3±8.9%v/v, respectively). To understand methanogenesis inhibition, the colorant waste was separated into sub-streams associated with different production operations and assayed individually, and CH4 production almost tripled when dye and oxidant levels were reduced. To explain CH4 yields, qPCR was used to quantify eubacteria and five methanogen groups among reactors. Colorant-fed units always had lower microbial abundances than shampoo-fed units, but Methanosarcinaceae levels were especially low in the low CH4 reactors. Further, these acetoclasts and hydrogenotrophic Methanobacteriales significantly correlated with CH4 yields across all reactors (r2=0.46, p=0.02 and r2=0.68, p=0.003, respectively). Waste-to-energy opportunities clearly exist for PCP wastes, although source separation is required to maximise gross CH4 yields.