Bioremediation technology, another strategy known for restoring degraded environments, utilizes beneficial microorganisms, including arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (NFB). Despite its potential, the biological processes of these microorganisms in contaminated sites remain poorly understood, hindering effective pollutant toxicity reduction. Establishing a connection between plant root systems and these microorganisms is crucial for enabling plant survival in heavy metal-contaminated soils. Narra (Pterocarpus indicus Willd.), a leguminous plant, typically associates with symbiotic nitrogen-fixing bacteria, forming nodules in the roots. Additionally, Narra forms a symbiotic relationship with AMF, phosphorus-fixing microbes, making it an ideal tree species for rehabilitating mined-out areas. In this study, five microbial biofertilizers, namely: MYKORICH®, MYKOVAM®, newMYC, newNFB, and combined newMYC+newNFB, plus a control were used to test their root colonization potential on Narra seedlings grown in nickel (Ni) and gold (Au) mined-out soils collected from Taganito Mining Corporation (TMC) and Manila Mining Corporation (MMC) in Claver and Placer, Surigao del Norte, Philippines, respectively. The results showed that newMYC had the highest root colonization in Ni mined-out soil, while MYKORICH® excelled in Au mined-out soil. The AMF spore count was highest in MYKORICH® for Ni mined-out soil and newMYC in Au mined-out soil. NFB colonization was highest in newMYC-treated seedlings for Ni mined-out soil and combined newMYC+newNFB for Au mined-out soil. The microbial biofertilizers utilized in this research, such as MY-KORICH®, MYKOVAM, newMYC, newNFB, and combined newNFB and newMYC, naturally occur in the environment and can be easily extracted. This cost-effective characteristic provides an advantage for mining companies seeking treatments for soil amelioration to rehabilitate mined-out areas.