Granulated micelle-clay complexes including the organic cation octadecyltrimethylammonium (ODTMA) were shown to be efficient in removal of total bacteria count (TBC) from water. Microwave (MW) heating of granules to restore bacterial removal was investigated. Drying of granules by MW required 20-fold less energy than by conventional heating. When water content of granules approached 10%, or less, their heating period by MW had to be below 1 min, e.g., 30 s, and less, in order to avoid ignition and irreversible structural changes. Structural and thermal properties of MW heated samples were studied by FT-IR spectra and thermo gravimetric analyses (TGA). Inactivation of bacteria in water was more efficient by MW than by conventional oven, or by electric plate. For elimination of bacteria from water, MW heating was at least five-fold more efficient than by conventional heating. The results have established an adequate regeneration procedure by MW heating at durations depending on the remaining percentage of water associated with the granules. Tests of first and second regenerations by MW heating, and HCl washing of columns, were carried out. It was concluded that MW treatment may be chosen for optimal regeneration of the granulated micelle-clay complex as an efficient and low-cost procedure.