Uncontrolled mine waste disposal globally poses severe environmental and health risks due to high concentrations of toxic substances like heavy metals and organic pollutants. This jeopardizes soil fertility and ecological balance. In this study, we adopted a novel approach based on the use of low-cost amendments that can be used in small to tailing sites for better plant growth and reducing health risks. On a 37-ha-old abandoned pyrrhotite mine site (Kettara) which was operated for 34 years near Marrakesh a high amount of tailing material low in organic C, high in salt contents, and contaminated by various heavy metals still exists. This material is low in fertility and is only patchily discovered by vegetation which should hinder the material of aeolian erosion. To increase the fertility of the material and improve vegetation growth, the soil material has to be improved by different organo-mineral amendments and their combinations as Marble waste (Mw), Clay (Cy), and Compost (Cp). To determine the impact of these amendments on plant growth the fast-growing Lupinus angustifolius L. a legume plant found close to the mining site, identified with the Regional Herbarium 'MARK' code: MARK-14861. This plant serves as a pivotal component in the comprehensive approach aimed at rehabilitating the soils surrounding the mining site. To identify the most effective organo-mineral amendment, we examined 65 combinations by mixing mine tailing soils with varying proportions (2.5%, 5%, 7.5%, or 10%) of the three distinct amendments and its combinations (Com), to identify the optimal rate for effective seeds germination and plant growth. Preliminary results on the germination index of L. angustifolius seeds revealed that four combinations (Com1: Cy2.5-Cp2.5-Mw10; Com2: Cy2.5-Cp5-Mw5; Com3: Cy7.5-Cp2.5-Mw7.5; and Com4: Cy10-Cp10-Mw10) maintained a high index due to improved soil properties. These combinations were used as the soil substrate material for a greenhouse experiment where plant growth, heavy metals accumulation, soil characteristics, and available metal content were determined. Our findings demonstrated that incorporating these four organo-mineral soil amendments into Kettara mine tailings led to a significant enhancement in plant growth. Notably, L. angustifolius plants exhibited a preferential accumulation of heavy metals in the root’s biomass (Cu: 565.60, Zn: 433.52, and Pb: 301.44 mg kg−1) with limited translocation to shoot parts (Cu: 37.44, Zn: 28.40, and Pb: 19.36 mg kg−1), particularly following the application of Com4. Furthermore, the properties of the mine soil were improved, including both neutralization of acidic soil pH (3 to ∼ 7) and reduction of metal elements bioavailability. Specifically, Com1, Com3, and Com4 effectively decreased the mobile fraction of metals in the tested mine tailings to exceptionally low levels achieving a reduction of 99% for copper, lead, and zinc, and 95% for arsenic. Our findings from this study indicated that our amendment holds promising potential for enhancing both plant growth and soil fertility, while simultaneously mitigating the mobility of heavy metals in heavy metal-contaminated acidic mine soils.