As urbanization expands, interest in understanding soil properties and functions in urban environments has also increased. Urban soils play an important role in the global carbon (C) cycle. Due to natural and human influences on various forms of C, quantifying soil inorganic carbon (SIC) becomes critical in urban areas. In this study, the suitability of diffuse reflectance mid-infrared Fourier-transform spectroscopy (mid-DRIFTS) to rapidly estimate calcite and dolomite concentrations was tested. Also, the effectiveness of HCl acid pre-treatment to remove carbonates to enable proper estimation of soil organic carbon (SOC) in urban soils was evaluated. Specific mid-infrared frequencies known to be associated with carbonates, i.e. dolomite and calcite, were identified, and specific peak areas were measured and calibrated with results obtained with the volumetric calcimeter method. Multiple linear regression was used to estimate total carbonates with peaks areas at 2930 cm−1, 2515 cm−1 and 730 cm−1 resulting in a 3.72% root mean squared error of an independent validation set (RMSEV). Greater prediction accuracy of calcite (875 cm−1) and dolomite (875 cm−1 and 730 cm−1) were achieved using single peaks in bivariate relationships resulting in RMSEV of 1.27% and 4.22%, respectively. Soil samples were treated with 1 M HCl for 24 h to remove carbonates, and total carbonate, dolomite, and calcite contents were estimated again using both volumetric calcimeter and mid-DRIFTS. The reduction in carbonate concentrations post-acid treatment was considerable (97% for dolomite, and 96% for calcite and total carbonates), but was not complete. Thus, this could compromise quantification of other soil carbon fractions such as total SOC. Using mid-DRIFTS peak areas of CO3−2 functional groups represents a robust alternative for rapid, fast, and low-cost laboratory measurements of soil carbonates, and this high-throughput approach may be used in assays aiming to minimize carbonate interference in SOC estimations.