Cicer arietinum L. (chickpea, or garbanzo bean) is one of the most consumed legumes worldwide. It is a rich source of carbohydrates, proteins, fibers, minerals and vitamins with very low cholesterol. From a nutritional point of view, despite the low content of fats, the seeds contain various unsaturated acids, such as linoleic and oleic acids, as well as bioactive compounds, like antioxidants, with reactive oxygen species-scavenging activities. It is known that long periods of storage can drastically affect the preservation of these compounds in seeds. For this reason, in the last few years, different methods have been tested with the aim of increasing the shelf life of economically relevant beans, seeds and cereals. A promising and eco-friendly alternative to traditional storage is the use of a controlled atmosphere, represented by N2-pressurized silos. The present study aims at evaluating the content of different compounds, e.g., fatty acids, proteins, vitamins, and molecules of nutraceutical interest, in chickpeas stored at ambient temperature in N2-pressurized silos (98.5 ± 0.5% (v/v)) and control ones (standard storage) in long-term kinetics (1 year). The results show the stable content of most compounds during the kinetics. However, vitamin E decreased in samples stored under both standard and controlled atmosphere conditions, with a more pronounced and significant decrease under standard conditions as compared to the controlled atmosphere. Additionally, samples stored under a controlled atmosphere show a total higher content of quinic, indole butyric and benzoic acid, as well as their derivates.