Two-stage anaerobic digestion and trace metals (TM) supplementation are promising techniques to improve biogas production. Fe2+ and Ni2+ can improve process stability since they are part of the cofactors of enzymes and microorganisms’ growth. This work attempted to evaluate the effect of Fe2+ and Ni2+ addition on H2-rich biogas production from organic solid waste and the CH4-rich biogas production from the acidogenic effluents (AEs) enriched with TM. The TM concentrations that enhanced the hydrogen yield in the batch were 0.25 mg/L of Ni2+ and 334 mg/L of Fe2+. These concentrations were evaluated in a two-stage system. The substrate for the batch tests and fermentative reactor (first stage) was OSW. The AE generated in the first stage was the substrate to produce CH4-rich biogas in the second stage. In the first stage, the productivity achieved was 1823 ± 160 mL H2/L/day. However, TM supplementation decreased productivity by 65% since the VS removal increased. Megasphaera genus predominated in the first stage. Regarding the methanogenic reactor, the undiluted AE without TM caused the fast decay of the process. Nevertheless, the reactor operated stably after using AE enriched with TM as a substrate, and CH4 yields increased by 42%. The highest productivity achieved in the second stage was 1278 ± 42 mL CH4/L/day, operating with an organic loading rate of 2.8 gVS/L/day. The genera Proteiniphilum, Thermovirga, DMER64, Anaerovorax, and Syntrophomonas predominated in the second stage. In conclusion, AE enriched with TM can be used to recover the stability of anaerobic digesters, increasing methane production.