Phosphorus (P) is a critical mineral nutrient for fish but its availability in plant-based aquafeeds is usually low. To avoid its over-supplementation and the consequent increase of feed cost, excretion and, ultimately, environmental pollution, phytase supplementation has been used as a strategy to improve the bio-availability of P present in plant-based feeds as well as overall nutrient digestibility. This study assessed the efficacy of a new generation bioengineered microbial phytase (HiPhorius™) on the growth performance, whole-body nutrient retention, nutrient digestibility, and P excretion of Nile tilapia (Oreochromis niloticus), European seabass (Dicentrarchus labrax), and gilthead seabream (Sparus aurata). In the trial, the fish were fed diets enriched with plant-protein rich diets. Five dietary treatments were tested over 94 days: a control diet (CTRL), three diets supplemented with phytase at graded doses (500, 1000, and 2000 FTY/kg feed), and a diet supplemented with either dicalcium or monocalcium phosphate (DCP/MCP). Results showed that feeds supplemented with the phytase led to a significant dose-dependent increase of final body weight, specific growth rate, and protein efficiency ratio (FBW, SGR, PER), and a significant reduction of FCR, in comparison to the CTRL treatment. Supplementation with the phytase also notably reduced P excretion down to 23.37 ± 1.69, 28.46 ± 4.07, and 18.86 ± 1.05 mg/kg/day of P excretion for Nile tilapia, European seabass, and gilthead seabream, respectively, as compared to the treatment with inorganic P supplementation (118.82 ± 3.87, 127.81 ± 2.58, and 117.09 ± 8.15 mg/kg/day of P excretion for Nile tilapia, European seabass, and gilthead seabream, respectively). Overall, results show that the phytase tested here is an effective strategy to contribute to the economic and environmental sustainability of aquaculture production in different fish species.