Soil contamination with metals is a major threat for the environment and public health since most metals are toxic to humans and to non-human biota, even at low concentrations. Thus, new sustainable remediation approaches are currently needed to immobilize metals in soils to decrease their mobility and bioavailability. In this work, we explore the application of discarded substrates from hydroponic cultivation, namely coconut shell and a mixture of coconut shell and pine bark, for immobilization of metals (Cd, Cr, Ni, Cu, Pb, Hg, Sb and As) in a naturally contaminated soil from a mining region in Portugal. The immobilization capacity of substrates (added to the soil at 5% mass ratio) was assessed both individually and also combined with other traditional agriculture soil additives (limestone and gypsum, at 2% mass ratio) and nanoparticles of zero-valent iron (nZVI) at 1–3% mass ratio. The overall results obtained after a 30-d incubation showed that the discarded substrates are a viable, economic, and environmental-friendly solution for metal remediation in soils, with the capacity of immobilization ranging from 20 to 91% for the metals and metalloids studied. Furthermore, they showed the capacity to reduce the soil toxicity (EC50 ∼ 6000 mg/L) to non-toxic levels (EC50 > 10000 mg/L) to the bacteria Aliivrio fischeri.