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A field experiment with winter wheat (<i>Triticum aestivum</i> L.) cultivation was conducted at the Research and Education Centre in Tomaszkowo, Poland (53°72′ N; 20°42′ E) in the years 2013–2016. Fertilisation with nitrogen at 150 and 200 kg ha⁻¹ and foliar application of manganese at 0.5 and 1.5 kg ha⁻¹ were the research factors. Wheat infestation by <i>Fusarium</i> spp. was determined by the habitat conditions during crop growth. Neither nitrogen nor manganese fertilisation affected the presence of <i>Fusarium</i> spp. symptoms on wheat ears, but the infestation intensity decreased with increasing nitrogen and manganese content in the grain. Only the level of deoxynivalenol (DON) was correlated with <i>Fusarium</i> spp. infestation. Increasing the nitrogen fertilisation rate from 150 kg ha⁻¹ to 200 kg ha⁻¹ resulted in higher grain contamination with toxins. Supplementation of nitrogen fertilisation with manganese reduced the number of mycotoxins in wheat grain. The grain yield was mainly affected by the varied weather conditions during the wheat-growing periods. Neither nitrogen nor manganese fertilisation differentiated the wheat grain yield. The objective of this study was to examine the impact of the weather conditions and nitrogen and manganese fertilisation on the grain yield, occurrence of <i>Fusarium</i> head blight and mycotoxin level in winter wheat grain.