Methods and systems for removing nitrogen during liquefaction of natural are provided. Methods of removing nitrogen include warming a predominantly methane stream in a methane cold box to provide a warmed predominantly methane stream; conducting at least a portion of the warmed predominantly methane stream from the methane cold box to a nitrogen removal unit comprising at least a first nitrogen removal column and a last nitrogen removal column, wherein the first nitrogen removal column is located upstream of the last nitrogen removal column; passing the warmed predominantly methane stream through the last nitrogen removal column to provide a refluxed warmed predominantly methane stream; and routing at least a portion of the refluxed warmed predominantly methane stream to the last nitrogen removal column.