Phytomining can be limited by low biomass productivity by plants or limited availability of soil metals. Ongoing research attempts to overcome these potential constraints and to make phytomining a successful commercial technique in the recovery of metals from polluted or naturally metal-rich soil by (hyper)accumulating plants. Recently, the benefits of combining phytoremediation with bioremediation, which uses beneficial microorganisms such as endophytic or rhizosphere bacteria and fungi for metal removal from soils, have been demonstrated. Metal-resistant microorganisms play an important role in enhancing plant survival and growth in these soils by alleviating metal toxicity and supplying nutrients. Furthermore, these beneficial microorganisms are able to enhance metal bioavailability in the rhizosphere of plants. An increase in plant growth and metal uptake increases the effectiveness of phytoremediation processes coupled with bioremediation. Here, we discuss how abiotic factors, such as the presence of metals in polluted sites or in naturally metal-rich (ultramafic) soils modulate activities of soil microbial communities. Then we introduce the concept of microbe-assisted phytomining and underline the role of plant-associated microorganisms in metal bioavailability and uptake by host plants that has attracted growing interest over the last decade. Finally, we present various techniques, including phenotypic, genotypic, and metagenomic approaches, which allow for characterizing soil microbial community structure and diversity and endophytic community in polluted or naturally metal-rich soils.