While biochar amendment is widely recommended as an excellent agricultural management practice, the biochar effect on the productivity of legume crops with symbiotic microorganisms has been poorly elucidated. Hence, a pot experiment was conducted by growing soybean with or without commercial rhizobia inoculation in an arbuscular mycorrhizal (AM) fungi rich sandy soil amended with wheat straw biochar produced respectively at 350 °C, 450 °C, and 550 °C. We tested the effect of biochar on soybean–rhizobia symbiosis and its impact on plant growth, leaf gas exchange and mycorrhizal colonisation. In brief, rhizobia inoculation, without biochar, increased net photosynthetic rate by 81% and plant total biomass by 44% compared to no inoculation (the control). Without inoculation, amendment of low-temperature biochar (350 ºC) resulted in higher (by 51%) plant biomass than high-temperature (550 °C) biochar. With rhizobia inoculation, low-temperature biochar decreased plant biomass by 9.3% compared to high-temperature biochar. Further, soybean with rhizobia under high-temperature biochar decreased plant biomass by 17% compared to rhizobia inoculation only but increased by 19% compared to the control. Soybean leaf gas exchange capacity and root morphological traits were consistent with plant biomass but symbiotic activity showed small differences among all the treatments. Overall, N-fixing rhizobia could alter the biochar effect on soybean in soil rich in indigenous AM fungi, depending on the pyrolysis temperature of the biochar used. Low-temperature biochar stimulated soybean growth greater than high-temperature biochar, while rhizobia shifted biochar’s positive effect.