Cobweb disease caused by members of the Cladobotryum genus is a major problem for growers of the white button mushroom (Agaricus bisporus). Synthetic fungicides such as prochloraz and metrafenone have been very successful at targeting and eliminating the pathogens that cause mushroom disease. However, prochloraz can no longer be used in the European Union (EU) from June 2023 and over-reliance on metrafenone has resulted in putative resistant pathogenic strains emerging. Prochloraz still showed good control of two different isolates of Cladobotryum mycophilum with efficacy values consistently reaching 70%. Metrafenone inhibited the growth of C. mycophilum isolate 618, which was isolated before metrafenone was introduced (efficacy 96%), but it failed to control C. mycophilum 1546, which was isolated after metrafenone was introduced, and which should now be classified as resistant. Two further C. mycophilum isolates from mushroom farms in 2019 also showed metrafenone resistance in vitro. In this work two biological control agents (BCAs) were investigated as potential environmentally sustainable alternatives to the fungicides prochloraz and metrafenone. The BCA Bacillus velezensis QST 713 was unsuccessful in controlling cobweb disease caused by C. mycophilum isolate 1546 while the BCA Bacillus velezensis Kos showed moderate control over two trials reaching 30–40% efficacy. Lower inoculum concentrations resulted in slightly lower but not significantly different disease levels across all treatments. Future trials with BCAs need to look at alternative methods to evaluate efficacy.