Citrus waste accounts for more than half of the whole fruit when processed for juice extraction. Among valorisation possibilities, anaerobic digestion for methane generation appears to be the most technically feasible and environmentally friendly alternative. However, citrus essential oils can inhibit this biological process. In this paper, the characteristics of citrus essential oils, as well as the mechanisms of their antimicrobial effects and potential adaptation mechanisms are reviewed. Previous studies of anaerobic digestion of citrus waste under different conditions are presented; however, some controversy exists regarding the limiting dosage of limonene for a stable process (24–192 mg of citrus essential oil per liter of digester and day). Successful strategies to avoid process inhibition by citrus essential oils are based either on recovery or removal of the limonene, by extraction or fungal pre-treatment respectively. Highlights: • Citrus waste can be valorised through anaerobic digestion for biogas production. • Citrus essential oils can inhibit the biological process of anaerobic digestion. • The reported mechanism suggests non-reversible inhibition. • Maximum citrus essential oil dosage in the literature ranges 24–192 mg Ldigester-1 d-1. • Liquid extraction and fungal treatment prior to anaerobic digestion avoid inhibition.