Fruit waste is a potential feedstock for biogas production. However, the presence of fruit flavors that have antimicrobial activity is a challenge for biogas production. Lactones, ketones, and phenolic compounds are among the several groups of fruit flavors that are present in many fruits. This work aimed to investigate the effects of two lactones, i.e., γ-hexalactone and γ-decalactone; two ketones, i.e., furaneol and mesifuran; and two phenolic compounds, i.e., quercetin and epicatechin on anaerobic digestion with a focus on methane production, biogas composition, and metabolic intermediates. Anaerobic digestion was performed in a batch glass digester incubated at 55oC for 30 days. The flavor compounds were added at concentrations of 0.05, 0.5, and 5 g/L. The results show that the addition of γ-decalactone, quercetin, and epicathechin in the range of 0.5–5g/L reduced the methane production by 50% (MIC50). Methane content was reduced by 90% with the addition of 5 g/L of γ-decalactone, quercetin, and epicathechin. Accumulation of acetic acid, together with an increase in carbon dioxide production, was observed. On the contrary, γ-hexalactone, furaneol, and mesifurane increased the methane production by 83–132% at a concentration of 5 g/L.