The objective of this study was to determine the effect of supplementing dough with phosphorolytic enzymes on the content of anti-nutritional factor, phytic acid, and on the spectrum of products of its hydrolysis, i.e. lower isomers of myo-inositol phosphates, in rye dough and rye bread. The product tested was supplemented with commercial, microbiological preparations of 3- and 6-phytase A and of phytase B during the proofing of dough. A high-pressure ion chromatography was applied to monitor changes in the profiles of myo-inositol phosphates during the fermentation of dough. The analysis of the content of phytate was performed using a colorimetric method with a Wade reagent. The highest reduction in the content of phytic acid was found in the case of 3-phytase A combined with phytase B. It was found that the cooperation between the 3-phytase and 6-phytase A with phytase B did not impact the dephosphorylation pathway of phytate, it only accelerated the hydrolysis process according to the bioconversion routes of phytase A. This fact was confirmed both by ‘enzyme – substrate’ model experiments and by the enzymatically modified breads. The enzymatic conversion results in forming physiologically active intermediates, among other things: Ins(1,2,6)P3 and Ins(1,4,5)P3, thus, the phytases A in cooperation with the phytase B could be, potentially, applied as bio-catalysts in the production of functional foods.