Background and aims It is known that the single and combined use of phosphate-solubilizing bacteria (PSB) and silicon (Si) have the potential to improve the uptake of phosphorus (P) by plants in calcareous soils. However, it was unclear which form of Si in soil would have the most profound effects on the uptake of P by wheat plant inoculated with PSB. Here we investigated the effect of Si fertilizer on chemical forms of Si and P uptake by wheat plant inoculated with PSB in a calcareous soil. Determining different forms of Si in calcareous soils with a low P supply is essential to better understand the capacity of these forms to supply wheat plant with P in the presence of PSB. Methods A pot trial in a completely randomized design with factorial arrangement in 3 repetitions under greenhouse conditions was adopted to investigate the effect of Si fertilizer alone or in combination with PSB on the uptake of P and Si by wheat plant grown on a calcareous soil with low available P. Experimental treatments included: Si factor at four levels of 0, 150, 300, and 600 mg Si kg(-1) from silicic acid source and PSB strains factor at three levels of B0 (control), Pseudomonas sp. FA1, and Bacillus simplex UT1. The impacts of Si levels and PSB on shoot and root dry weight and the wheat shoot uptake of Si and P were measured. Also, the chemical forms of Si in wheat rhizosphere and non-rhizosphere soil and the regression models of the variables were studied to better understand the mechanisms of this process. Results With increasing the levels of Si, the plant available Si with the lowest level, adsorbed Si, and amorphous Si with the highest level in both the rhizosphere and non-rhizosphere soil increased. In addition, Si fertilization-mediated increase at level of the soil Si fractions was intensified in the presence of PSB strains. The highest plant available Si (75.50 mg Si kg(-1) soil) was obtained from the treatment of 600 mg Si kg(-1) soil in the presence of Pseudomonas sp. FA1. The combined application of Si and PSB strains also increased the wheat shoot dry weight by 3.5 times compared to the control treatments. The use of Si alone at level of 300 mg Si kg(-1) also increased the wheat shoot content of P by 2.3 times compared to the control treatment. However, the combined application of Pseudomonas sp. FA1 and Si at level of 600 mg Si kg(-1) increased the wheat shoot content of P by 4 times compared to the control treatment. According to the correlations among the studied parameters, in addition to the expected positive correlation between plant available Si of wheat rhizosphere soil and the measured parameters, a positive and significant correlation between adsorbed Si of wheat rhizosphere soil and the shoot uptake of Si (r(2) = 0.84, P < 0.01) and the shoot uptake of P (r(2) = 0.58, P < 0.05) was also observed in this study. Conclusions The information on the distribution of different forms of Si and the availability of P following the combined use of PSB strains and Si in this study (e.g., the role of rhizosphere adsorbed Si in increasing the wheat shoot uptake of P) may help in better management of P-fertilization in calcareous soils.