The effect of chemical pre-treatment on identification and semi-quantification of clay minerals by X-ray diffraction (XRD) analysis was studied in soils (0–15 cm) collected from four ongoing long-term (31 years) experiments located at Ludhiana (Inceptisol), Jabalpur (Vertisol), Pantnagar (Mollisol) and Ranchi (Alfisol) under five treatments with different combinations of organic and inorganic nutrient sources. From each soil, clay (with pre-treatment) and colloidal organo-mineral fraction or COMF (without pre-treatment) were isolated for XRD analyses. The identification and semi-quantification of clay minerals from pre-treated clay have already been reported (Das et al. in Sci Total Environ 684:682–693, 2019). Here, the aim was to identify the soil type(s) where such pre-treatment can be avoided without compromising accuracy of mineral identification and semi-quantification. Among the soil orders, Alfisol showed the least variation in X-ray diffractograms between clay and COMF, whereas variation was the highest in Vertisol. Irrespective of soil orders, illite and illite-rich interstratified minerals (IRM) and kaolinite and kaolinite-rich interstratified mineral (KRM) peaks were least affected by the presence of organic C and amorphous Fe oxide in COMF, whereas peaks of smectite or smectite-rich interstratified minerals (SRM) were affected the most. Chlorite peak was distorted due to chemical pre-treatment with large amounts of H2O2 for removal of organic matter from Mollisol. Overall, the results indicated that identification and semi-quantification of clay minerals by XRD can be done with reasonable accuracy even without chemical pre-treatment in Alfisol dominated by KRM and IRM. In Inceptisol, Vertisol and Mollisol, the same appeared to be less appropriate.