This study aimed to develop a mitigation strategy for the formation of 2-monochloropropane-1,3-diol esters (2-MCPDE), 3-monochloropropane-1,2-diol esters (3-MCPDE), and glycidol fatty acid esters (GE) during palm oil refining. Single physical refining was the starting point (the control) for this study. Experimental treatments including a double refining repeating the entire single refining process (T1), double refining with a high-low deodorization temperature (T2), and double deodorization (T3) with similar temperature settings as T2 were performed. Compared with the control experiment, T2 successfully reduced the formation of GE by 87%; in particular, the second degumming and bleaching were crucial for eliminating GE. Both 2- and 3-MCPDE were formed prior to the deodorization process in all treatments. MCPDE concentrations remained stable throughout the refining process and, hence, they require a different mitigation approach as compared to GE. These results provide useful insights which can directly be implemented by the oil industry.