A field study was performed to evaluate the effect of mineral (NPK) and organic-based fertilizers such as compost (C), manure (FYM) and meat and bone meal (MBM) on the appearance (dimensions and color) of spring wheat kernels and on the total content in grain of main its phytochemicals (polyphenols, carotenoids and tocochromanols) and phenolic acids composition. Total phenolic compounds were determined using the Folin-Ciocalteu assay after alkaline hydrolysis of grain and carotenoids were analyzed spectrophotometrically. Composition of tocochromanols and phenolic acids was determined using RP-HPLC techniques. Only insignificant differences in the appearance of kernels and small changes in the content and composition of grain phytochemicals were noted between the studied fertilization systems. Among the analyzed phytochemicals the greatest variation was observed in the group of polyphenol compounds, with a stated increase of their total content of 6.7 and 11.2% in grain fertilized with MBM and compost, respectively. Simultaneously the grain from organic fertilization contained significantly less phenolic acids, and the decrease in their content ranged from 10.0% for FYM to 24.8% for MBM+EM-1. Organically and conventionally fertilized grain had similar amounts of tocochromanols and carotenoids. Comparison of MBM and MBM+EM-1 variants showed that application of effective microorganisms decreased carotenoids and tocochromanols content by 8.5 and 9.7%, respectively.