There is a great need for simple methods for digestate management for potential household sanitation systems based on anaerobic digestion of minimally diluted fecal waste in countries that lack safe sanitation. Herein, a full-scale three-stage filter for nitrogen and phosphorus removal from anaerobic digester effluent was implemented in Madagascar. It included a trickling filter with crushed charcoal (for aerobic nitrification), a submerged anaerobic filter with bamboo chips (for denitrification), and a submerged filter with scrap iron (for phosphorus removal). All filter materials were sourced locally. Three parallel replicate systems were operated in two sequential 8-week phases for a total of 16 continuous weeks. Though the influent feed was not as expected, with much of nitrogen in the feed coming in as organic N and not as NH3-N, the filters still removed 38-49% of total incoming nitrogen. The filters achieved high rates of nitrogen transformation along with removing solids (73-82% turbidity removal), chemical oxygen demand (67-75% removal), and phosphorus (31-50% removal). Overall, the reaction rates from this full-scale study were in line with previous lab-scale investigations with scaled-down systems, supporting their application in real-world scenarios. Based on this study, simple effluent filters can support nutrient removal for small-scale and onsite fecal sludge treatment systems.