Global climate change is anticipated to shift the soil bacterial community structure and plant nutrient utilization. The use of biochar amendment can positively influence soil bacterial community structure, soil properties, and nutrient use efficiency of crops. However, little is known about the underlying mechanism and response of bacterial community structure to biochar amendment, and its role in nutrient enhancement in soil and plants under elevated CO2. Herein, the effect of biochar amendment (0, 0.5, 1.5%) on soil bacterial community structure, spinach growth, physiology, and soil and plant nutrient status were investigated under two CO2 concentrations (400 and 600 μmol mol−1). Findings showed that biochar application 1.5% (B.2.E) significantly increased the abundance of the bacterial community responsible for growth and nutrient uptake i.e. Firmicutes (42.25%) Bacteroidetes (10.46%), and Gemmatimonadetes (125.75%) as compared to respective control (CK.E) but interestingly abundance of proteobacteria decreased (9.18%) under elevated CO2. Furthermore, the soil available N, P, and K showed a significant increase in higher biochar-amended treatments under elevated CO2. Spinach plants exhibited a notable enhancement in growth and photosynthetic pigments when exposed to elevated CO2 levels and biochar, as compared to ambient CO2 conditions. However, there was variability observed in the leaf gas exchange attributes. Elevated CO2 reduced spinach roots and leaves nutrient concentration. In contrast, the biochar amendment (B2.E) enhanced root and shoot Zinc (494.99%–155.33%), magnesium (261.15%–183.37%), manganese (80.04%–152.86%), potassium (576.24%–355.17%), calcium (261.88%–165.65%), copper (325.42%–282.53%) and iron (717.63%–177.90%) concentration by influencing plant physiology and bacterial community. These findings provide insights into the interaction between plant and bacterial community under future agroecosystems in response to the addition of biochar contributing to a deeper understanding of ecological dynamics.