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A phase separation/continuous flow macrocyclization protocol eliminates the need for high-dilution conditions and can be used to prepare gram quantities of biologically relevant macrocyclic lipid structures. The method presents several green advantages towards macrocycle synthesis: (1) the prevention of unwanted oligomers and waste, (2) a reduction in the large quantities of toxic, volatile organic solvents and (3) the use of PEG as an environmentally benign reaction media. Macrocycles could be synthesized in high yields (up to 99%) in short reaction times (1.5 h) and on gram scales without the need to alter the reaction conditions.