•Strain T1-17 and biochar increased the edible tissue biomass of the two vegetables.•T1-17 and biochar reduced the edible tissue Cd and Pb uptake of the vegetables.•T1-17 and biochar decreased the available Cd and Pb contents of the rhizosphere soil.•T1-17 increased the ratio of IAA-producing bacteria and small aggregates in the soil.•Biochar+T1-17 was best to increase the biomass and decrease tissue Cd or Pb uptake. The effects of a plant growth-promoting Neorhizobium huautlense T1-17, biochar, and their combination on the biomass and Cd and Pb accumulation of Chinese cabbages and radishes and the mechanisms involved were characterized. T1-17 increased the biomass and reduced the above-ground tissue (Chinese cabbages) or root (radishes) Cd and Pb contents of the seedlings compared to the control. T1-17 and biochar+T1-17 significantly increased the edible tissue biomass (ranging from 56% to 112%) of the two vegetables compared to the control. T1-17, biochar, and their combination significantly reduced the edible tissue Cd and Pb contents (ranging from 46% to 86%) and total Cd and Pb uptake (ranging from 16% to 78%) of the two vegetables compared to the controls. Biochar+T1-17 had higher ability to increase the biomass and decrease the edible tissue Cd (Chinese cabbages) and Pb (radishes) contents than T1-17 or biochar. Furthermore, T1-17, biochar, and their combination significantly decreased the water-soluble (ranging from 32% to 88%) and DTPA-extractable (ranging from 14% to 51%) Cd and Pb contents in the rhizosphere soils compared to the controls. Notably, biochar+T1-17 had higher ability to decrease the water-soluble Cd and Pb contents of the rhizosphere soils than T1-17 or biochar. T1-17 and biochar+T1-17 significantly increased the ratios of small soil aggregate particles (<0.25mm) of the rhizosphere soils of the two vegetables and negative correlation between the ratios of small soil aggregate particles and the DTPA-extractable Cd and Pb contents was observed. Furthermore, T1-17 and biochar+T1-17 significantly increased the ratio of IAA-producing bacteria in the rhizosphere soils of the two vegetables. The results showed the synergistic effects of T1-17 and biochar on the increased edible tissue biomass and decreased available Cd and Pb in the soils and Cd and Pb uptake of the vegetables. The results also suggested that T1-17 and biochar+T1-17 increased the edible tissue growth and reduced the edible tissue Cd and Pb uptake of the vegetables through increasing the proportions of plant growth-promoting bacteria and small soil aggregates in the rhizosphere soils.