Porcine cysticercosis (PC) caused by the larval stage of a zoonotic tapeworm Taenia solium, is known to pose serious economic losses and public health risk among smallholder pig production communities. The present study was conducted to determine prevalence and associated risk factors for PC in smallholder pig production systems in Mbeya region, the major pig rearing region of Tanzania. A cross-sectional survey employing a random sample of 300 pig keepers from 30 villages of Mbozi and Mbeya Rural districts, Mbeya region were used to evaluate pig production systems and practices. Concurrently, 600 male and female pigs of different age categories were randomly selected and examined for PC using lingual examination method and antigen enzyme-linked immunosorbent assay (Ag- ELISA). The overall pig level PC prevalence in Mbozi district was 11.7% (95% CI = 8.5–15.8%) and 32% (95% CI: 27–37.5%) based on lingual examination and Ag-ELISA, respectively. In Mbeya Rural district, the prevalences were 6% (95% CI: 3.8–9.3%) and 30.7% (95% CI: 25.8–36.1%) by lingual examination and Ag-ELISA, respectively. In Mbozi district 46% of the households were found infected (one or more infected pigs) and the corresponding figure was 45% for Mbeya Rural district. The agreement between lingual examination and Ag-ELISA was poor ( < 0.40). There were no significant differences in the prevalence of PC in different sex categories of pigs. Significant risk factors associated with PC preva- lence were free roaming of pigs (OR = 2.1; 95% CI = 1.3–3.6; p = 0.006), past experience of porcine cysticercosis in the household (OR = 2.6; 95% CI = 1.5–4.8; p = 0.002), increased age of pig (OR = 1.9; 95% CI = 1.2–3.0), slatted raised floor in pig pen (OR = 8.4; 95% CI = 1.0–70.0), in-house origin of the pig (OR = 1.6; 95% CI = 1.1–2.5) and sourcing of water from rivers (OR = 3.1; 95% CI = 1.6–6.3; p < 0.001) and ponds (OR = 5.0; 95% CI = 1.2–21.7; p = 0.031). This study has clearly revealed a high sero-prevalence of PC in the study area, which imposes a major economical and public health burden to the smallholder pig farmers. The study also points to a number of important risk factors in smallholder pig management that may be addressed (e.g. confinement, quality of pens and water sources) in future interventions and educational campaigns for control of T. solium.