The First Stage of French Vertical Flow Constructed Wetlands (FS-FVFCW) offers a sustainable solution for treating septage. The system operates through distinct phases: start-up, full operation and final rest. During full operation, factors such as feeding duration, rest periods and percolate impounding significantly affect performance. This study assessed the performance of a pilot-scale Modified FS-FVFCW in Northern Tropical Andes, from start-up to closure stages under three operational scenarios. These scenarios varied in planted/unplanted conditions and percolate drainage/impounding. A four-month start-up phase proved adequate for vegetation growth and adaptation, achieving over 50% COD removal efficiency. Percolate retention (impounding) during operation notably improved COD and TS removal, increasing efficiencies from 49% to approximately 90% for COD and from 39% to around 70% for TS. Plant presence contributed to mosquito control and odour reduction but had minimal impact on removal efficiencies. The pilot demonstrated significant dewatering potential, with sludge deposit samples showing water content below 76% across all scenarios after 24 h; and a 10% reduction in VS/TS ratio during the operational resting period. After a 5-month closure, the sludge deposit layer exhibited organic matter content similar to long-rested sludge, albeit with persistent faecal contamination.