This paper describes an unusual type of abnormal coloration caused by the fungal species Phoma glomerata (P. glomerata) detected in samples of commercially available mozzarella cheese produced from cow’s milk. The presence of this fungus in dairy and cheese products has already been reported by other authors, along with other fungal contaminants; however, it has never been associated to specific alterations of cheeses. This is the first report of a macroscopic alteration of a soft cheese due to P. glomerata. Mozzarella cheese from four packages (two sealed and two already opened, three of which with evident macroscopic alterations) was analyzed by means of ISO methods for the detection of the main bacterial and fungal contaminants of cheese products. Culture tests carried out according to the ISO 21527-1:2008 method revealed presence of P. glomerata (from 1,100 CFU/g to 45,000 CFU/g). In addition, in both the previously opened packages, Acremonium spp. (100 CFU/g), Alternaria spp. (100 CFU/g), Pseudomonas fluorescens (25,000 CFU/g) and Pseudomonas putida (2,400 CFU/g) were also isolated. In sample N°4, contamination by P. glomerata was present, but in the absence of macroscopic changes. These results show that P. glomerata is able to contaminate mozzarella cheese, causing macroscopically visible alterations of the product; this may have serious consequences in terms of sales. With regard to the possible effects on human health, further studies are needed in order to assess the toxic effect of the fungus. As a result of the episode described, the Italian health authorities issued a RASFF (Rapid Alert System for Food and Feed) early warning notice, a key E.U. tool to ensure the cross-border flow of information in order to react swiftly when risks to public health are detected in the food chain.