Catalytic and physicochemical properties of microbial phytase sources may differ, affecting phosphorus (P) release and subsequently the productive and reproductive performance of layers. The current study aimed to evaluate the impact of bacterial and fungal phytase sources on layer productivity, egg production, biochemical blood indices, and reproductive morphology. For this purpose, 360 Bovans brown hens at 42 weeks of age were randomly allocated into 4 experimental groups, each with 15 replicates of 6 hens. The first group (control) was fed a basal diet with 4.6 g/kg available P. In contrast, the second, third, and fourth groups were fed diets treated with 3.2 g/kg available P, supplemented with either 5000 FTU/kg of bacterial E. coli (QuantumTM Blue 5G), fungal Aspergillus niger (VemoZyme® F 5000 Naturally Thermostable Phytase (NTP)), or fungal Trichodermareesei (Yemzim® FZ100). Dietary supplementation of bacterial and fungal phytases did not affect the productive performance or egg quality criteria, except for increased shell weight and thickness (p < 0.05). Serum hepatic function biomarkers and lipid profiles were not altered in treated hens, while calcium and P levels were increased (p < 0.05) related to the controls. Ovary index and length, and relative weight of oviduct and its segments were not influenced. The contents of cholesterol and malondialdehyde in the yolks from treated birds were lower compared to control hens, while calcium and P content increased (p < 0.05). Conclusively, bacterial and fungal phytase sources can compensate for the reduction of available P in layers’ diets and enhance shell and yolk quality without affecting productive performance, and no differences among them were noticed.