The disclosure relates to a gradient twin column recycling chromatography method that is used to separate a mixture containing closely eluting compounds. In one embodiment, a sample includes a primary organic compound and one or more impurities that closely elute with the primary organic compound. A gradient mobile phase is initially used to remove unwanted early eluting and late eluting impurities from the sample. After the gradient removal of some of the impurities is complete, the remaining mixture of the primary organic compound and the closely eluting impurities are separated using recycle chromatography methodology with an isocratic mobile phase.