To quantify the citrate induced transformation of short range order (SRO) minerals, a controlled column experiment was conducted with three soils representing three soil orders. The soils were saturated with six concentrations of citric acid (CA) viz. 0, 5, 10, 20, 40, 100 mg L−1 in 0.01 M CaCl2 solution, with an addition of fresh CA at 15, 30, 45, 60 days. After 60 days the whole soil was collected and separated into clay and clay-humus complex of colloidal and non-colloidal fractions and analyzed for SRO. Maximum formation of amorphous ferri-alumino silicate (AFAS) was observed in Alfisol treated with 10 mg L−1 citric acid for both the size fractions. Citric acid concentration of 20 mg L−1 resulted in maximum formation of oxalate extractable allophane plus imogolite and total oxides in Inceptisol colloidal clay. Crystalline iron content in colloidal clay was decreased with increasing concentration of citric acid. Maximum ferrihydrite and crystalline iron were observed in Alfisol in both the clay fractions. It may be concluded that SRO minerals formed or dissolved depending upon the concentration of CA and the most favourable concentration for maximum SROs formation was in the range of 20–40 mg L−1.