The present invention is directed to a method or preparing fatty acid alkyl esters from fatty acids contained in co-product streams, or waste or recycled fatty acid stock. The present method utilizes an acidic resin to convert the fatty acid stock into esters. The present method encompasses the use of reactive simulated moving bed chromatography, wherein above about 95 percent of the fatty acid stock is converted to fatty acid alkyl esters. The present method has been optimized to separate the ester product from the raffinate stream formed during the chromatographic process, thereby improving the yield of the esterification and preventing acid hydrolysis of the ester.