Field-applicable, high-quality, and low-cost diagnostic tools are urgently needed for Taenia solium. The aim of this paper is to describe the design, challenges, and rationale for the design of a diagnostic accuracy study in low-resource community settings in Zambia. The trial was designed as a prospective study with a two-stage design to evaluate a new point-of-care test (TS POC) for the detection of taeniosis and (neuro)cysticercosis. Participants within randomly selected households were tested with the TS POC test (index test). Participants who tested TS POC positive for taeniosis and/or cysticercosis and a subset of the negatives were requested to give blood and stool samples for reference testing, and to undergo clinical examination and a cerebral CT scan. The difficulties of conducting a clinical trial in settings with limited research and neuroimaging infrastructure as well as peculiarities specifically related to the disease (low prevalence of taeniosis and the lack of a gold standard) were taken into consideration for the design of this study. The two-stage design increased the efficiency of the study by reducing the number of samples, clinical examinations, and CT scans. Simplified flows and sampling processes were preferred over complex follow-up and randomization systems, aiming to reduce bias and increase the generalizability of the study.