Washing with organic acids and dissolved organic carbon (DOC) is a promising technique for effective removal of potentially toxic metals from agricultural soils and the two key factors are the screening of inexpensive, high-efficiency, and environmentally friendly washing agents and the safe treatment of waste eluent. We used extracts from agro-forestry wastes (pineapple peel, lemon peel, grapefruit peel and gardening crabapple fruit) to develop a facile two-stage sequential washing method (extracts and/or citric acid (CA) and coupled with extracts) and regenerated waste eluent. The washing efficiencies of Cd and Cu were significantly increased by pineapple peel (PP) using two-stage sequential washing with the sequence of PP + CA-PP > CA-PP > PP-PP. The potential pollution risk from soil Cd was lowered by 33.0% from moderate to low risk, and soil nutrient contents increased. 80.9% of Cd and 81.3% of Cu in waste eluent were efficiently removed by the PP residues. The removal mechanisms of metals in soils and eluents by PP washing agents and residues can be attributed to acid activation, cation exchange and complexation between metal ions and carboxyl groups. Therefore, the PP extracts and residues are potentially suitable for the removal of Cd and Cu from polluted agricultural soils and washing waste eluents.