Mycotoxins can pose a threat to biogas production as they can contaminate the feedstock used in biogas production, such as agricultural crops and other organic materials. This research study evaluated the contents of deoxynivalenol (DON), zearalenone (ZEA), fumonisin (FUM), and aflatoxin (AFL) mycotoxins in maize silage prior to it being processed in a biogas plant and in digestate produced at the end of the anaerobic digestion (AD) process. In the experiment, three samples of silage were collected from one silage warehouse: Variant 1 = low contamination, Variant 2 = medium contamination, and Variant 3 = heavy contamination, which were subjected to investigation. A significantly reduced biogas production was recorded that was proportional to the increasing contamination with molds, which was primarily due to the AD of silage caused by technologically erroneous silage treatment. The AD was connected with changes in silage composition expressed by the values of VS content, sugar content, lactic acid content, acetic acid content, and the ratio of lactic acid content to acetic acid content. The production of biogas and methane decreased with the increasing contents of NDF, ADF, CF, and lignin. The only exception was Variant 2, in which the content of ADF, CF, and lignin was lower (by 8–11%) than that in Variant 1, and only the content of NDF was higher (by 9%) than that in Variant 1. A secondary factor that also correlated with changes in the composition of the substrate was the development of undesirable organisms, which further contributed to its degradation and to the production of mycotoxins. It was also demonstrated in this study that during the AD process, the tested mycotoxins were degraded, and their content was reduced by 27–100%. Only the variant with low mold contamination showed a DON concentration increase of 27.8%.