Organic waste can provide an alternative to synthetic fertilisers for maintaining productivity with limited environmental impact. Our research evaluates the potential use of processed animal waste in corn fertilisation, which may represent a partially closed nutrient cycle of importance in a sustainable agricultural system. The objective of this study was to evaluate the quantity and quality of fat obtained from corn grain fertilised with meat and bone meal (MBM) produced from animal waste. A static field experiment using MBM was conducted at the Experimental Station in Tomaszkowo (53°71′ N, 20°43′ E), Poland. The field experiment was conducted in 2014–2017 with continuous corn cultivation. The course of weather conditions in the years of this study influenced the fat content, with the lowest amount found in 2016. The application of fertilisers in the form of MBM and mineral fertilisation resulted in a slightly lower fat content compared to the variant without fertilisation. The application of mineral fertilisers and MBM influenced an increase in the content of the predominant C18:2 acid compared to the variant without fertilisation, while the opposite was shown for C18:1 cis-9 acid. The fertiliser variants are most correlated with fat yield and total polyunsaturated fatty acids. The fertiliser variants in their effects on fat yield, fat content, fatty acid profiles, and their ratios can be divided into three groups, which were related to the effects of organic fertilisers during the years of this study. The use of meat and bone meal as fertilisers cannot be regarded as a factor in increasing the fat content of corn grain. Meat and bone meal applied over several years to the same field in the quantities required to achieve optimum yield can be an element that shapes fatty acid profiles.