Caffeine and chlorogenic acids are two major bioactive compounds available in coffee cherry which offers health beneficial effects to human. However, US Food and Drug Administration recommends caffeine to be safer within a limit of consumption with 400 mg/d. Therefore, there has been a demanding interest in the development of coffee extract with limited caffeine content along with significant levels of chlorogenic acids. Caffeine act as a good complexing agent with vitamins, nucleic acids, phenolic compounds, and other biomolecules that could affect their biological properties. In this study we investigate the structural analysis of caffeine enriched whole coffee cherry extracts CEWCCE1 (70% caffeine and 6% chlorogenic acids) and CEWCCE2 (40% caffeine and 40% and chlorogenic acids) by using 1H and 13C NMR spectroscopy. The changes in 1H chemical shift data in NMR spectra of CEWCCE1 and CEWCCE2 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 isomers and caffeine were investigated at different ratios of caffeoylquinic acid and caffeine in solution. 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.