Palm oil is a type of vegetable oil which presents a variety of applications including food, energy, and international trading. However, one of the major concerns associated with palm oil uses as a food ingredient is the significant amount of processing contaminants, such as monochloropropanediol esters (MCPDE) and glycidyl esters (GE) which are formed during the refining process. These contaminants may pose a health risk to consumers due to their carcinogenicity. Thus, mitigation strategies have been studied to reduce these substances in palm oil. In this study, we investigated the effect of the application of an aqueous washing step, as a mitigation strategy, prior to deodorization in three different palm oil cultivation systems: organic, conventional and certified palm oil by the Roundtable on Sustainable Palm Oil (RSPO). In addition, we evaluated the quality parameters after the application of the washing step. For the organic, conventional and RSPO palm oil samples, the aqueous washing step reduced approximately 41%, 34% and 36% of the 3-MCPDE, respectively. The levels of 2-MCPDE for the organic, conventional and RSPO palm oil presented a reduction of 55%, 41% and 32%, respectively. The GE levels are considerably low for all the deodorized palm oils, and presented no statistically significant difference (p > 0.05). Besides, the quality parameters such as free fatty acids, color, and OSI met the recommended limits. Therefore, the aqueous washing could be used as a supplementary strategy to reduce these contaminants from palm oil.