The low capacity of degraded soils to provide phosphorus (P) and potassium (K) to plants makes cultivation unviable in these areas. Biochar can increase nutrients availability and improve the physical conditions of soil to maintain their availability over time, including within soil macroaggregates, where P and K are less susceptible to losses. The aim of this study is to understand, how biochar application can change P and K availability in aggregates of degraded soils. The experiment is carried out under controlled conditions following the factorial scheme 2 × 3 × 5 × 2 + 4, corresponding to two classes of soil, three biochars produced from different raw materials (including stems of elephant grass, EGB, and two types of agricultural wastes: eucalypt stalks, ESB, and sugarcane bagasse, SBB), five rates of biochar, two times and four control treatments. At the end of each time, soil aggregates are divided into two classes by size (macroaggregates and microaggregates) and then P and K availability are measured. The results show that biochar can be a powerful tool to increase P and K availability in soil aggregates. EGB is the most efficient biochar to increase P and K availability, followed by SBB and ESB biochars.