The availability of low-cost biometric hardware sensors and software makes it possible to rapidly, affordably and securely sample and store a unique and invariant biological signature (or biometric 'template') of participants in research and trials. This has applications in consent, linkage of case reporting forms collected at different times, and in confirmation of participant identity for purposes of safety monitoring and adherence to international data laws. The use of mobile electronic data collection software has recently become commonplace in clinical trials and research. A raft of tools based on the open-source ODK project now provide diverse options for data management that work consistently in low resourced settings, but none have built-in functionality for capturing biometric templates. In this study, we report the development and testing of a novel open-source app and associated method for capturing and matching biometric fingerprint templates during data collection with the popular data platforms ODK, KoBoToolbox, SurveyCTO, Ona and CommCare. Using data from more than 1000 fingers, we show that fingerprint templates can be used to link data forms with high accuracy and that this accuracy increases with the addition of multiple fingerprints on each data form. By focussing on publishing open-source code and documentation, and by using an affordable (<$50) and mass-produced model of fingerprint sensor, we are able to make this platform freely available to the large global user community that utilises ODK and related data collection systems.