In laboratory experiments, Lepidium sativum L. and Mentha spicata L. were grown in compost spiked with mercury. After cultivation for 20 and 68 days, respectively, translocation factors of 0.05 ≤ TF ≤ 0.2 (Lepidium sativum) and accumulation factors of 2.2 ≤ AF ≤ 12 (Mentha spicata) were recorded. Plants were then harvested and used as feedstock for bench-scale anaerobic digesters. The reactors operated in continuously-stirred batch mode for a period of ten days. Inhibition of anaerobic biogas production was apparent with one sample set evidencing mercury-induced bacteriostatic toxicity. Otherwise, ex-situ characterization of digestate showed that the reactors were within stable operating range. A canola oil-sulphide polymer derived from bio-waste was also used as an intermediary treatment stage to test its capacity for extracting mercury from half the samples prior to anaerobic digestion, and also from the post-experimentation reactor digestate. The polymer removed mercury from digestate with a 40–50% efficacy across all samples, suggesting its potential as a sludge clean-up option. Anaerobic digestion combined with staged polymer extraction offers a potential route for the disposal of phytoremediation crops and ultimately the recovery of mercury, coincident with the production of a bioenergy vector.