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Coffee cherry is a rich source of caffeine and chlorogenic acids. In this study we investigate the structural analysis of caffeine-enriched whole coffee cherry extracts, CEWCCE by using ¹H and ¹³C NMR spectroscopy. The changes in ¹H chemical shift data in NMR spectra of CEWCCE compared to pure caffeine indicated the formation of complexes between caffeine and chlorogenic acids in aqueous solution. The effect of complexation on the peak position of caffeoylquinic acid and caffeine resonance with increasing addition of caffeine was investigated. 2D NOESY experiments show the presence of cross-peaks that are due to the proximity of chlorogenic acid and caffeine molecules in stable complexes in protic solvents. The quantification data of caffeine by ¹H qNMR was found to be in close agreement with the data obtained by HPLC analysis.