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A cross-sectional study was carried out to determine risk factors for prevalence of common endo- and ectoparasites of pigs kept by smallholder farmers in Mbozi and Mbeya (Rural) districts of Mbeya Region, in Tanzania. A total of 482 pigs from 220 households of 16 villages, eight in each district were randomly selected and examined. Prevalence of Taenia solium cysticercosis was 11.5%, gastrointestinal nematodes 63.7% and ectoparasites 21.2% based on Ag-ELISA, McMaster technique and full body searches/ear scrapings, respectively. Nematode eggs identified were strongyles (Oesophagostomum spp. and Trichostrongylus spp.), Ascaris suum, Trichuris suis and Strongyloides ransomi with prevalence of 57.4%, 17.5%, 5.3% and 1.1%, respectively. Four groups of ectoparasites were identified, i.e. lice (Haematopinus suis), ticks (Rhipicephalus spp., Amblyomma spp., Haemaphysalis spp. and Boophilus spp.), fleas (Ctenocephalides canis) and mites (Sarcoptes scabiei var. suis and Demodex phylloides), with prevalence of 19.1%, 2.1%, 0.4%, and 1.2%, respectively. Pigs in Mbeya (Rural) District had higher odds for porcine cysticercosis (OR = 2.63, 95% CI: [1.22–5.55]). Poor pen hygiene and infrequent antiparasitic treatment were identified to be risk factors for prevalence of nematode infections (OR = 1.95 [1.09–3.52] and OR = 1.78 [1.06–2.94], respectively). The odds for high nematode burdens increased in cases of poor pen hygiene (OR = 4.20 [2.54–6.62]) and poor feed quality (OR = 3.7 [1.66–8.33]). Pigs not treated with antiparasitic drugs within the last three months had higher odds for ectoparasite (OR = 4.0 [1.78–9.09]) and lice infestations (OR = 8.33 [1.96–14.28]) than treated pigs. This study has shown that parasitoses constitute a major burden for smallholder pigs in Mbeya Region and major risk factors included infrequent antiparasitic treatment, poor pen hygiene and poor feed quality. Cost-effective intervention strategies are needed to improve pork production, secure pig welfare and ensure safe pork for human consumption.