Essential heavy metals are vital for crop development, but high concentrations and prolonged exposure can be detrimental. Non-essential heavy metals, even at trace levels, can act as potent toxins for plant cells by mimicking essential metal ions and disrupting cellular functions. This similarity between essential and non-essential heavy metals complicates efforts to mitigate their toxic effects and to prevent the bio-magnification of harmful metals like cadmium, lead, chromium, nickel, and arsenic. Heavy metal toxicity not only affects plant yields, but also poses significant risks to human health through the consumption of contaminated crops. Here we analyze the role of microorganisms in ameliorating the accumulation of toxic heavy metals in crop fruits, either by sequestering metals in root cells or by immobilizing them in the soil. This summary highlights the similarities between heavy metal transporters and phytochelatin synthesis in plants and microorganisms, advocating for the use of microbial genes to engineer plants and enhance food security. Additionally, we explore the trends and perspectives in the field of plant growth-promoting bacteria (PGPB), which aid the adsorption of toxic metals by plants. Microbial biotechnology holds immense potential for tailoring metal transport processes, storing metals in vacuoles, inactivating metals, and limiting the availability of undesirable metals to plants. However, many opportunities remain unexplored in engineering plants with microbial elements. This emerging research area warrants further investigation, along with efforts to communicate the benefits of engineered organisms, addressing concerns and demonstrating controlled management and application of these technologies to ensure their safe and effective use.