A cross-sectional study was carried out to determine the prevalence and associated risk factors of parasitic infections in pigs kept under smallholder farming system in Angónia district, Tete Province, Mozambique. A total of 262 pigs from 133 households of six villages were randomly selected. From each pig blood, faecal samples, full body searches, and skin scrapings were conducted to determine the prevalence of Taenia solium (using Ag-ELISA), gastrointestinal (GI) parasites, and ectoparasites respectively. A questionnaire survey was administered to smallholder pig farmers to assess their knowledge and perceptions of health and pig management and an observational study was conducted to determine their pig management practices. The overall prevalence of porcine cysticercosis by Ag-ELISA was 12.6%, GI nematodes 21.4%, Eimeria spp. 8.0% and ectoparasites 37.8%. Four helminths species namely, Metastrongylus spp., Hyostrongylus spp., Oesophagostomum spp., Trichostrongylus spp., were identified from by copro culture, and through faecal egg count, Ascaris suum and Trichuris suis were identified. Haematopinus suis, Rhipicephalus spp. and Echidnophaga gallinacea were found with a prevalence of 32.4%, 7.6%, and 6.9%, respectively. The only significant risk factor identified to be related to the parasite prevalence was pig origin (village), for both gastrointestinal parasites (OR = 10.81[0.81–57.27]) and ectoparasites (OR = 7.06[1.42–35.03]). This study provided evidence that parasitic infections in pigs constitute a major burden for smallholder pig farmers in Angónia district, and that porcine cysticercosis is a public health threat in the area and immediate attention is needed for control and prevention of the parasite.