Biofertilizer as amendment has growing awareness, little attention has been paid to the bioremediation potential of indigenous heavy metal-resistant microbes, especially when isolated from long term polluted soil, as a bioinoculant in biofertilizer. They are type of versatile nutrient provider and soil conditioner that is cost competitive, highly efficient with nondisruptive detoxifying capability. Herein, we investigated the effect of biofertilizers containing indigenous cadmium (Cd)-resistant microbial consortia on rice growth and physiological response. The Thai rice cultivar PSL2 ( Oryza sativa L.) was grown in Cd-enriched soils amended with 3% biofertilizer. The composition of the biofertilizers’ bacterial community at different taxonomic levels was explored using 16S rRNA gene Illumina MiSeq sequencing. Upon Cd stress, the test biofertilizer had maximum mitigating effects as shown by suppressed photosynthetic pigment loss, modulated proline content and enzymatic antioxidants, thereby allowing increased plant dry biomass (up to 115% and 112% in shoots and roots, respectively) and reduced tissue Cd content (up to 68% and 65% in shoots and roots, respectively), as compared to the non-amended control. These phenomena might be attributed to increased soil pH, EC, CEC and organic matter, as well as enriched beneficial detoxifiers, i.e., Bacteroidetes, Firmicutes, and Proteobacteria in the biofertilizers. The test biofertilizer was effective in ameliorating Cd phytotoxicity by improving soil biophysicochemical traits to limit Cd bioavailability, along with adjusting physiological traits such as antioxidative defense. This study first demonstrated that incorporating indigenous Cd-resistant microbe derived-biofertilizer could restrict Cd contents and consequently enhance plant growth and tolerance in polluted soil.