The growing demand for natural rubber products has driven the expansion of rubber plantations in recent decades. While much attention has been given to studying the long-term effects of rubber and rubber-based agroforestry systems on surface soil properties, there has been a tendency to overlook changes in soil properties in deeper layers. Our study addresses this gap by examining alterations in nitrogen (N), phosphorus (P), and metal ion levels in deep soil layers resulting from the prolonged cultivation of rubber and rubber-based agroforestry systems. We found notable shifts in soil NH4+ and NO3− concentrations within the 0–30 cm soil layer across different-aged rubber and rubber-based agroforestry systems. Particularly in mature systems, NO3− and available P levels were close to zero below 30 cm soil depth. Introducing Flemingia macrophylla into young rubber plantations increased soil NH4+ and NO3− in the 0–90 cm soil layer and available P in the 0–10 cm soil layer. Over the long term, cultivation of rubber plantations increased the depletion of total P in the 0–50 cm soil layer, available iron (Fe) and manganese (Mn) in the 30–90 cm soil layer, available copper (Cu) and zinc (Zn) in the 0–90 cm soil layer, accompanied by a decrease in soil pH and increase in exchangeable aluminum (Al) in the 0–90 cm soil layer. Notably, soil exchangeable Al levels exceeding 2.0 cmol kg−1 appeared to induce aluminum toxicity. Furthermore, soil pH below 5.2 triggered a sharp release of exchangeable Al within the 0–90 cm soil layer of rubber plantations, with soil available P nearing zero when exchangeable Al levels assed 7.3 cmol kg−1. Our findings underscore the profound impact of long-term rubber plantation cultivation on surface and deep soil properties. Addressing soil degradation in these deep soil layers poses significant challenges for future soil restoration efforts.