The study investigated and compared welfare conditions and gastrointestinal (GI) parasites distribution among organic (ORG) and conventional (CONV) farms in central Italy. Five ORG and five CONV farms were assessed for animal welfare with an adapted version of the AssureWel protocol. Faecal samples collected from the rectum of the animals both in ORG (n = 150) and CONV (n = 150) were analysed using conventional copromiscroscopy. The presence of skin damages in the rear legs was significantly predominant (p p < 0.001). Anthelmintics were used regularly in 4/5 CONV and 0/5 ORG farms. In 2 CONV farms (40%) and 4 ORGs (80%) at least one animal tested positive for GI parasites. No significant differences in parasites prevalence emerged (ORG = 10.7%; CONV = 8%). These data indicate that ORG farming does not influence parasite prevalence and animal welfare status.