Rapid worldwide urbanization has created peri-urban environments that often lack services and infrastructure for water and sanitation. Globally, around 4.5 billion people do not have access to safely managed sanitation, as is often the case in such environments. Efforts to develop appropriate sanitation alternatives in these contexts recognize the value of understanding users’ preferences and interaction with their sanitation systems, however, the traditional tools for assessing technology usage and adoption are based on physical observation, which presents limitations. In this work, we developed a toilet sensor to identify usage patterns of pour-flush toilets by quantifying flushing and defecation events. The device has a methane gas sensor, IR distance sensor and a motion sensor connected to a microcontroller. Its small footprint allows for unobtrusive installation inside a toilet bowl and operates battery-powered for about 5 days depending on usage patterns. To evaluate the sensor performance, units were installed for a field trial in nine participants’ households in a Mexican peri-urban community and an algorithm for automated data analysis was developed. Surveys were also conducted to benchmark the sensor performance and determine the potential value of the approach. Results showed that on average people underreported their daily toilet usage by two events compared to the measurements and they flushed only 75% of the time after defecation. By monitoring the usage of the current pour-flush toilets lacking piped water and sewerage and complementing the data with users’ feedback, we can gain an understanding of the existing limitations so more suitable sanitation alternatives can be proposed.