Abstract: Corn (Zea mays L.) is important for food security in much of Ecuador. Small-scale farmers are using nitrogen (N) fertilizer without technical advice based on soil, crop, and climatologic data. The literature lacks studies where tools that can quickly assess management practices’ effects on N uptake, N use efficiency, and risk of N losses to the environment in high-altitude mountain systems are validated. We tested corn response to fertilizer application and the capability of the Nitrogen Index to assess N dynamics within a conservation agriculture production system in a mountainous area of Ecuador. Responses to fertilizer were tested across six sites in the Bolivar province. Steep slopes and declining soil productivity make conservation agriculture a promising option in this area. However, N availability is limiting for corn production and better information is needed to optimize the system. Corn responded to fertilizer application with an average increase of 30 kg ha−1 corn grain per every 1 kg of N ha−1 applied (P < 0.001). The data suggest that N leaching increased with fertilizer application for areas with precipitation greater than 900 mm. The Nitrogen Index for Ecuador was able to quickly assess management practices’ effects on N uptake (P < 0.001), N use efficiency (P < 0.001), and risk of N losses. It could be used to increase use of best management practices in these systems.