The monitoring of the microbial quality of fresh products in the industrial environment has mainly focused on bacterial indicators. Protozoa, such as Giardia duodenalis, Cryptosporidium spp., Toxoplasma gondii, and Cyclospora cayetanensis, are routinely excluded from detection and surveillance systems, despite guidelines and regulations that support the need for tracking and monitoring these pathogens in fresh food products. Previous studies performed by our laboratory, within the scope of the SafeConsume project, clearly indicated that consumption of fresh produce may be a source of T. gondii, thus posing a risk for the contraction of toxoplasmosis for susceptible consumers. Therefore, preliminary work was performed in order to assess the microbiological quality of vegetables, highlighting not only bacteria (Escherichia. coli, Listeria monocytogenes, and Salmonella spp.), but also the zoonotic protozoa G. duodenalis and Cryptosporidium spp. Although all samples were found to be acceptable based on bacteriological parameters, cysts of G. duodenalis and oocysts of Cryptosporidium spp. were observed in vegetables. Moreover, it was possible to genetically characterize G. duodenalis positive samples as assemblage A, a genotype that poses risks to human health. Although these are preliminary results, they highlight the need to include protozoa in the microbiological criteria for foodstuffs, as required by EU Law No. 1441/2007, and to improve inactivation and removal procedures of (oo)cysts in fresh produce and water.