The objective of this study was to evaluate the effect of mixtures of the phosphate industry’s by-products and sewage sludge on some heavy metals (Pb, Zn and Cd) in the soil–plant system and the microbial load (bacteria, fungi and actinobacteria) in the soil. The experimental layout was a completely randomized design with ten treatments and four replications. The treatments consist of a combination of five substrates: phosphogypsum (PG), phosphate sludge (PS), sewage sludge (SS), phosphate waste rocks (PWR) and original mine topsoil (TS). Heavy metals analysis, phytoextraction efficiency (PEE) and bioconcentration factor (BCF) were carried out for three Ryegrass cuts. The microbial load of each treatment was determined at the end of the experiment. The results showed that the Pb, Zn and Cd contents of the treatments were well below the permissible limits given in the literature. The highest BCF and PEE were with treatment T4. Furthermore, bacteria, fungi and actinobacteria were significantly influenced by the different proportions of by-products used in the treatments, with the highest richness observed for the T4 treatment. For a successful reclamation of mine sites, it would be useful to determine the speciation of metals in the soil solution and the microbial genetic diversity.