The transesterification process used for biodiesel production yields glycerol as a prominent byproduct. Given glycerol's adverse effects on engine performance and longevity, regulatory standards, such as those set by SNI and international authorities, restrict free glycerol content in biodiesel to below 0.02 wt.% or 200 ppm. Consequently, the removal of glycerol has become a critical step in biodiesel production. Traditional purification methods are energy-intensive and generate substantial wastewater, prompting the exploration of alternative solutions like membrane separation technology. Ceramic microfiltration membranes, renowned for their exceptional thermal, chemical, and mechanical durability, have emerged as a prominent choice. The development and application of a cost-effective Alumina-Kaolin ceramic microfiltration membrane for glycerol removal in biodiesel signify a promising advancement in water purification processes. The current study was conducted to evaluate the microfiltration performance of the Alumina-Kaolin ceramic membrane, investigate the impact of the membrane’s microstructure on separation performance, and explore cleaning strategies aimed at enhancing flux recovery ratio (FRR). The microstructure analysis through SEM and BET demonstrated pores in the membrane, featuring a 3.375 m2/g surface area, 30.367 % porosity, and 0.18 μm pore size. Several tests employed using different glycerol and water concentration in the feed of 1000 ppm, 5000 ppm and 10000 ppm. The evaluation gave high glycerol rejection rates of 92.07%, 98.52% and 98.94% for the respective feed concentrations with the permeate flux of 65.42 [l/(m2h)], 61.09 [l/(m2h)] and 52.91 [l/(m2h)] respectively. The microstructure of alumina-kaolin membrane could separate the larger particles of glycerol-water droplets and gave high separation performance. As the flux decline ratio increased (from 2.13% to 20.86%) due to rising glycerol concentration (1,000 to 10,000 ppm), cleaning became crucial for flux recovery. Employing various agents, benzalkonium chloride notably enhanced alumina-kaolin flux recovery ratio (FRR) to 98.17%.