Chestnut shells (CS), the principal by-product of the chestnut processing industry, contain high concentrations of flavonoids and other polyphenols with huge interest for the nutraceuticals field. Nonetheless, the bioaccessibility and bioactivity of phytochemicals can be influenced by their digestibility, making it imperative to evaluate these activities prior to application of CS as a nutraceutical ingredient. This work aims to appraise the effects of in vitro simulated gastrointestinal digestion on the bioaccessibility, bioactivity, and metabolic profiling of CS. An increase in the total phenolic and flavonoid contents, antioxidant/antiradical properties, radical scavenging capacity, and inhibition on acetylcholinesterase activity was evidenced during in vitro simulated digestion. Metabolomic profiling by LC-ESI-LTQ-Orbitrap-MS revealed changes during the simulated digestion, particularly in phenolic compounds (46% of total compounds annotated), lipids (22%), phenylpropanoids (9%), organic acids (7%), carbohydrates (5%), nucleosides (5%), amino acids (4%), and alcohols (1%). Phenolic acids (gallic acid, syringic acid, and hydroxyphenylacetic acid) and flavonoids (epicatechin) were the major polyphenolic classes identified. The heatmap-positive correlations highlighted that the bioactivity of CS is closely related to the phenolic compounds and their bioaccessibility. These findings suggest the reuse of CS as a potential nutraceutical ingredient with antioxidant and neuroprotective effects, encouraging the use of appropriate extraction and/or encapsulation techniques to enhance the bioaccessibility of phenolic compounds.