In our study the presence of bacteria, yeast, and microscopic fungi was evaluated. Three forms of corn silage were made including silage without additive, silage with microbial additive (lactic acid bacteria), and silage with nutritional additive (urea). Silage additives were applied to the matter within the recommended dosage, then the matter was ensiled into plastic bags and stored at a constant temperature. After 5.5 months of storage, average samples for microbial and mycotoxins analysis were taken. From microbiological points, the plate count agar method for enumeration of total count of bacteria, lactic acid bacteria, enterococci, yeasts, and microscopic fungi and mass spectrometry for microbiota identification were used. In total, 43 species of bacteria and yeasts and 6 genera of microscopic fungi were identified from all samples of corn silages. The most isolated species were Lentilactobacillus buchneri and Kazachstania exigua from bacteria resp. yeasts and Aspergillus and Penicillium from microscopic fungi. Mycotoxins were determined by HPLC-MS/MS and divided into two groups as regulated and emerging. In the corn silages only Fusarium mycotoxins were observed. All corn silages, regardless of the addition of the additive, were the highest in nivalenol content. Deoxynivalenol and beauvericin with the highest concentrations were present in silage with urea. Although the mycotoxins content of the variants changed, these changes were not statistically significant. In general, addition of lactic acid bacteria Lentilactobacillus buchneri and Lacticaseibacillus casei and urea as silage additives affect the microbial diversity; however, the hygienic quality of whole crop corn silage was not negatively changed.