The occurrence of diseases in the cultivation of maize (Zea mays L.) leads to the loss of grain yield and the simultaneous deterioration of its quality. Fungi of the genus Fusarium spp. pose the greatest threat to maize cultivation. These fungi occur at all stages of the plant’s development, causing Fusarium seedling blight, root rot, foot rot, and ear rot, including grains. Therefore, the aim of the conducted field studies was to determine the influence of selected agriculture factors on mycotoxin contents in maize grain and ear core. Moreover, it should be noted that the presence of mycotoxins in food products in terms of legal regulations is quite a fundamental barrier both in domestic and international trade. The field experiment was carried out at the Department of Agronomy of Poznań University of Life Sciences, on the fields of the Experimental and Educational Unit in Swadzim, Poland, in 2013–2014, in four field replicates. The study involved the following factors: soil sowing preparation method, types of variates, and fertilization method, all of which shape mycotoxin accumulation. The results indicated that the main effects of years were significant for all observed traits for both the core and grain. The concentrations of deoxynivalenol, nivalenol, and zearalenone were higher in 2014 than in 2013 for both core and grain. The concentrations of fumonisin B1 and fumonisin B2 were higher in the first year of study for core and grain. The direct sowing of maize significantly affects plants’ health status, expressed by an increase in mycotoxin accumulation. Traditional hybrid SY Cooky characterized higher values of observed traits than “stay-green” hybrid Drim (except fumonisin B2 for cob). The positive effect of the row method of NP fertilizer application is based on a decrease in mycotoxin content.