The essential oils in citrus waste poses challenges for the anaerobic digestion application to energy recovery from these wastes due to the potential to inhibit the bioprocess. The two-stage system is a practical alternative to overcome these limitations of anaerobic co-digestion of citrus peel waste and wastewater. This study proposes to overcome drawbacks associated with the use of these substrates in anaerobic digestion by separating the phases, performing parameters optimization of the methanogenic stage. To obtain optimized conditions for the methanogenic stage, the Rotational Central Composite Design (RCCD) and Response Surface Methodology (RSM) were applied, evaluating the effects of diluting the Fermentation Reactor Content (FRC) of the first stage (35.7%–100%) and alkalinization (up to 0.60 g sodium bicarbonate.gCOD−1), in methane production and organic matter removal. Values from 2100.4 to 6320.6 mLCH4.L−1 were obtained in the experimental design assays, with no inhibition identified by the high substrate concentration, nor by the limonene content (1.5–5.0 mg.L−1). Lower dilution of the fermentation reactor content (90%–100%) resulted in higher accumulated methane production, while the variation in the alkalinization did not imply significant effects on this response. The optimized condition for maximum production potential was obtained with 99.3% of fermentation reactor content and 0.58 gNaCHO3.gCOD−1, reaching a production of 6549.7 mLCH4.L−1, with organic matter removal (rCOD) of 87.1%, and 58.6% of reduction in solid waste content. For this condition, acetogenic metabolism predominance was observed, in the conversion of butyric acid and propionic acid into acetic acid. In the analysis of the microbial community of the optimized condition assay, a high relative abundance of hydrolytic and acidogenic bacteria (AUTHM297, Lachnospiraceae, and Hungateiclostridiaceae) was observed, as well as methanogenic archaea related to acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis (Methanoregula, Methanolinea, Methanomassiliicoccus, Candidatus Methanomethylicus, and Methanofolis).