The safety and quality of animal feed are often unknown concerning the content of fungi and mycotoxins. Animal feed may be infested with fungi, leading to contamination with mycotoxins, which pose a potential risk to human and animal health. Currently, the feeding of pigs is mainly based on cereals and soy as protein components. In order to reduce the cost of feed production, other protein sources are used in addition to soy. To assess the health of pig feeds containing guar meal in their composition, a study was conducted to evaluate the presence of toxigenic fungi (culture and qPCR method) and mycotoxins (HPLC). Eight complete feeds produced on the farm containing locally produced feed materials including soybean meal and guar meal as protein components were investigated. The results of the mycobiome analysis showed that the tested feed mixtures were characterised by a high diversity of fungi, with saprophytic species clearly dominating. The qPCR analysis confirmed the presence of Fusarium and P. verrucosum fungi in the mixtures. Chemical tests of mycotoxin content confirmed the presence of Fusarium mycotoxins: DON, 3-AcDON, ZEA, T2 and OTA. Barley grain and guar meal were responsible for the contamination of the feed with the toxins DON, 3-AcDON, ZEA and OTA, while in the case of the T2 toxins wheat grain and to a lesser extent the premix were responsible. The above correlations were confirmed by a correlation analysis that took into account the different levels of the feed components. Overall, it should be emphasised that the feeds were contaminated with mycotoxins to a low degree, which confirms their high quality. The storage conditions favoured the development of saprotrophic mycoflora and prevented the development of toxigenic species.