Unexpected volume changes manifested in the soil beds due to accidental release of alkalis from industrial establishments has become a major challenge. The neogenic formation that leads to volume changes due to physicochemical reactions between clay minerals and alkalis need to be addressed. The current article focusses on the possibility of using alternate by-products such as ground granulated blast furnace slag (GGBFS) and flyash (FA) for controlling the swell induced in alkali transformed kaolinitic clays, ATKC’s (i.e., red earth and kaolin). Results indicate that ATKC’s exhibited unexpected changes in swelling behavior upon inundation with water and alkali (4N NaOH) solutions. ATKC’s were later amended with FA and GGBFS to address the swelling phenomena. Marked reduction in swelling was noticed in ATKC’s with FA (10% and 20%) and GGBFS (10% and 20%). Reduction of about 40% of overall swelling was noted in alkali transformed red earth (ATR) when treated with 10% FA and 50% reduction with 10% GGBFS. Further, treatment of ATR with 20% FA and 20% GGBFS, decreased swelling to about 82% compared with ATR-4N. In case of alkali transformed kaolin (ATK), 57% and 56% reduction in swelling were observed with addition of 10% FA and 10% GGBFS, respectively. At 20% FA and GGBS content, reduction in ATK-4N swelling was 75% and 90%, respectively. Thermo Gravimetric–Differential Thermal Analysis (TG–DTA), X-ray Diffraction, and Scanning Electron Microscopy (SEM) analysis confirmed the alterations in ATKC are stabilized with FA and GGBFS.