In this study, the anammox process was applied for the first time to the treatment of ammonium-rich liquid residues produced by the two-stage anaerobic digestion of food waste (2sAD-FW); such residues may represent a significant environmental issue if not properly managed. A granular anammox reactor was fed with a progressively increasing share of partially nitritated 2sAD-FW wastewater. An alternative operating strategy based on partial by-pass of the partial nitritation unit was tested, in order to regulate the influent NO2/NH4 molar ratio without chemical addition. High nitrogen removal efficiency (89 ± 1%) and negligible nitrite discharge rates were achieved, together with high nitrogen removal rate/nitrogen loading rate (NRR/NLR, 97 ± 1%) and stable specific anammox activity (0.42 ± 0.03 gN2-N/gVSS d). The observed NH4-removed/NO2-removed/NO3-produced molar ratio was in agreement with anammox stoichiometry, as confirmed by the low contribution (<5%) of denitrification to nitrogen removal. Moreover, the possibility of using digital color characterization of granular biomass as a novel, simple tool for the monitoring of anammox biomass enrichment and process performance was investigated under dynamic conditions, using real wastewater: changes in granule color correlated well with the increasing share of 2sAD-FW wastewater in the influent (R2 = 83%), as well as with the decrease of anammox biomass abundance in the reactor (R2 = 68%). The results suggest that anammox may be successfully integrated into a 2sAD-FW system, thus enhancing its environmental sustainability.