Textiles made of natural fibers, both contemporary and historical, are at constant risk of degradation caused by, among others, microbial enzymatic activity. Fungi, bacteria, or actinomycetes are capable of producing proteolytic and cellulolytic enzymes, enabling microbial growth on textiles and leading to their decay. Ensuring proper storage conditions, including the usage of protective materials, allows long-term preservation of historical textiles in a good condition. These studies involved a broad microbiological analysis in order to verify whether high-density polyethylene (HDPE) materials can protect historical textiles during their storage. The results demonstrate interesting differences in microbial counts between washed textiles stored without HDPE covers and those stored in such covers; the latter presented considerably higher counts of microorganisms. However, when textiles had previously been sterilized, HDPE covers helped maintain appropriate microbiological purity. A considerable portion of historical textile collections, particularly exceptional silk liturgical vestments or burial garments, are kept by church institutions and stored in sacristies, treasuries, or other church rooms. The specificity of these places, both cultural and related to the age of the buildings themselves, makes them exceptional environments for storing textiles. To date, these places have rarely been researched, particularly in microbiological aspects. The analysis recounted below encompasses qualitative and quantitative assessment of fungi and bacteria present in the air of the treasury of the Wawel Royal Cathedral in Krakow, Poland, as well as the analysis of their destructive potential.