Background: An interventional study named Malakit was implemented between April 2018 and March 2020 to address malaria in gold mining areas in French Guiana, in collaboration with Suriname and Brazil. This innovative intervention relied on the distribution of kits for self-diagnosis and self-treatment to gold miners after training by health mediators, referred to in the project as facilitators. Objective: This paper aims to describe the process by which the information system was designed, developed, and implemented to achieve the monitoring and evaluation of the Malakit intervention. Methods: The intervention was implemented in challenging conditions at five cross-border distribution sites, which imposed strong logistical constraints for the design of the information system: isolation in the Amazon rainforest, tropical climate, and lack of reliable electricity supply and internet connection. Additional constraints originated from the interaction of the multicultural players involved in the study. The Malakit information system was developed as a patchwork of existing open-source software, commercial services, and tools developed in-house. Facilitators collected data from participants using Android tablets with ODK (Open Data Kit) Collect. A custom R package and a dashboard web app were developed to retrieve, decrypt, aggregate, monitor, and clean data according to feedback from facilitators and supervision visits on the field. Results: Between April 2018 and March 2020, nine facilitators generated a total of 4863 form records, corresponding to an average of 202 records per month. Facilitators’ feedback was essential for adapting and improving mobile data collection and monitoring. Few technical issues were reported. The median duration of data capture was 5 (IQR 3-7) minutes, suggesting that electronic data capture was not taking more time from participants, and it decreased over the course of the study as facilitators become more experienced. The quality of data collected by facilitators was satisfactory, with only 3.03% (147/4849) of form records requiring correction. Conclusions: The development of the information system for the Malakit project was a source of innovation that mirrored the inventiveness of the intervention itself. Our experience confirms that even in a challenging environment, it is possible to produce good-quality data and evaluate a complex health intervention by carefully adapting tools to field constraints and health mediators’ experience.