A comprehensive view of whole-brain amino acid levels hold the potential to provide valuable insights into the brain's state, given the mutual interconnections through metabolism, food intake, and neurotransmission. We tested this concept by evaluating free amino acid levels in single Drosophila brains across 24h and at two different ages. A large proportion of these amino acids displayed time-of-day variations, and a subset exhibited age-dependent variations. Cross-correlation analysis of the datasets confirmed broad time-of-day and age dependent interconnections between amino acids. Factor Analysis of Mixed Data revealed further data structuration along key amino acids. For example, 50% of the variance could be accounted by an inverse coupling between gamma-aminobutyric acid and several essential amino acids during the active phase, linking food intake and sleep. This proof of concept emphasizes the value of combining multivariate analysis to whole-brain amino acid levels evaluation, shedding potentially new light on sleep-wake regulation and aging.