Phytate is a substance that has been considered mainly as an antinutrient, but at the same time it is a significant source of phosphorus and has several useful health-related properties that could be exploited. In this respect, a field experiment was conducted to study the effect of organic and conventional cropping systems with nitrogen (N) and phosphorus (P) amounts from 0 to 150 kg ha⁻¹ and 0–25 kg ha⁻¹, respectively, in six years (2017–2022) of weather conditions on phytate content in Estonia. Winter wheat had a higher phytate content of 1.9 ± 0.13 g 100 g⁻¹ compared to spring barley with 1.1 ± 0.05 g 100 g⁻¹. Fertilization with N or P did not affect phytate content in grains. Harvest year weather conditions (precipitation and air temperature) had a strong effect on phytate content. at a specific stage of plant development. Higher values of growing degree days in June and July, which sum in the experimental period varied between 609 and 978 °C, increased phytate content in winter wheat grains (flowering and grain filling stage), while the impact on spring barley phytate content was opposite (heading and flowering stage). Future research should study phytate content in grains grown on varying fertility level soils.