Biogas digestates can be applied to hydroponics via nitrification. However, the low solubility of phosphorus in digestates can cause phosphorus deficiency in plants. Here, we hypothesized that acidophilic nitrification might prevent this deficiency by dissolving phosphorus in the digestate. Acidophilic and neutrophilic nitrification were conducted at a pH of 3.27 and 6.25 using biogas digestates from food wastes. Acidophilic nitrification dissolved about 3.5 times more phosphorus than neutrophilic nitrification, but the increased acidity also reduced the nitrification rate, resulting in residual ammonium. We then grew lettuce hydroponically with filtrates of these digestates. The growth performance suggested that the increased phosphorus improved growth and that the residual ammonium did not inhibit it. Acidophilic nitrification was shown to be effective for use in hydroponics, particularly to alleviate phosphorus deficiency. These findings should provide new insights into resource recycling, which is essential in both urban and space environments.