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This study was carried out, at both laboratory- and pilot-scale, to investigate whether the presence of phosphorus affects the nitrification process during aerobic digestion of aquaculture/aquaponic solid waste. Results from the laboratory-scale aerobic digestions indicated that nitrification did not occur throughout the entire bioprocessing period (21 days) in aerobic bioreactors containing phosphorus. The mineralization process in laboratory-scale aerobic bioreactors which did not contain phosphorus, on the other hand, followed the typical non-inhibited nitrogen mineralization (i.e., release of ammonium, NH4+ followed by oxidation into nitrate, NO3−). Results from pilot-scale aerobic digestions confirmed that the presence of phosphorus did impact the nitrification of aquaculture/aquaponic solid waste. However, analytical data and modeled parameters revealed that the presence of phosphorus significantly (P = 0.0406) delayed the onset of nitrification (lag period of 9.2 days for aerobic bioreactors without the presence of phosphorus compared to 29.3 days for aerobic bioreactors containing phosphorus, corresponding to a delay period of 3 weeks) but did not influence (P > 0.05) the nitrification kinetic parameters (i.e., maximum nitrate concentration (99.5–101.1 mg/L) and maximum rate of nitrate production (11.3–19.6 mg/L/day)).