•High barrier packaging can be used as a replacement for vacuum packaging without loss of quality for 18 months of storage.•It is possible to anticipate by up to 3 months the identification of chemical changes that would only be noticed through sensory analysis after six months of storage.•Choline and glycerophosphocholine were associated with changes in aging of green coffee packaged in paper bags. Nuclear magnetic resonance (NMR) was used to identify metabolic changes in green coffee beans stored in 3 different packages. Sensory and NMR analyses were performed at 0, 3, 6, 9, 12 and 18 months of storage. The decrease in the sensory quality of beverages by aging was more pronounced in the paper bags after 6 months of storage. High barrier bags and vacuum packs were able to maintain quality for 18 months of storage, regardless of the coffee processing method. The NMR technique allowed the differentiation of coffee packed in paper bags from the 3rd month of storage. These results indicate that it is possible to anticipate by up to 3 months the identification of changes that would otherwise only be noticed through sensory analysis after six months of storage. Choline and glycerophosphocholine are the main chemical compounds associated with the changes observed in the storage of green coffee in paper bags.