This study investigated gastrointestinal parasites and ticks in cattle and goats at Akinyele Abattoir, South-Western Nigeria, to address gaps in epidemiology, species identification, and pathology. Faecal samples and adult parasites were collected from 61 cattle and 35 goats, between March and July 2025. The employed morphological techniques and 18S rRNA gene sequencing confirmed the presence of Strongyles, Eimeria spp., Fasciola gigantica, Paramphistomum cervi, and Moniezia expansa. Strongyles dominated across hosts, with higher burdens in Red Bororo and White Fulani cattle, and Red Sokoto and West African Dwarf goats. The multinomial logit model revealed the susceptibility of males and younger animals to multiple infections. Goats carried higher egg/oocyst counts than cattle. Gross lesions in cattle included mucosal hyperaemia, catarrhal to haemorrhagic enteritis, and nematode presence, while goats exhibited mucosal reddening, thickening, and catarrhal enteritis, with severe pathology linked to dictyocaulosis and schistosomiasis, caused by Dictyocaulus spp. and Schistosoma spp., respectively, or chronic fluke infection. Molecular analysis confirmed Fasciola gigantica, Paramphistomum cervi, and Moniezia expansa with 99–100% sequence identity, supporting phylogenetic relationships. Fasciola was absent in cattle but found in goats. Our findings highlight breed, sex, and age vulnerabilities; the value of combined diagnostics; and the need for targeted deworming, pasture hygiene, and selective breeding, to improve livestock health and reduce zoonotic risks. Future research addressing seasonal dynamics, anthelmintic resistance, genetic markers of host resistance, and spatial determinants of parasite exposure to strengthen livestock health and One Health outcomes is encouraged.