Chestnut shells (CS) are an agronomic waste generated from the peeling process of the chestnut fruit, which contain 2.7–5.2% (w/w) phenolic compounds and approximately 36% (w/w) polysaccharides. In contrast with current shell waste burning practices, this study proposes a CS biorefinery that integrates biomass pretreatment, recovery of bioactive molecules, and bioconversion of the lignocellulosic hydrolyzate, while optimizing materials reuse. The CS delignification and saccharification produced a crude hydrolyzate with 12.9 g/L of glucose and xylose, and 682 mg/L of gallic acid equivalents. The detoxification of the crude CS hydrolyzate with 5% (w/v) activated charcoal (AC) and repeated adsorption, desorption and AC reuse enabled 70.3% (w/w) of phenolic compounds recovery, whilst simultaneously retaining the soluble sugars in the detoxified hydrolyzate. The phenols radical scavenging activity (RSA) of the first AC eluate reached 51.8 ± 1.6%, which is significantly higher than that of the crude CS hydrolyzate (21.0 ± 1.1%). The fermentation of the detoxified hydrolyzate by C. butyricum produced 10.7 ± 0.2 mM butyrate and 63.9 mL H2/g of CS. Based on the obtained results, the CS biorefinery integrating two energy products (H2 and calorific power from spent CS), two bioproducts (phenolic compounds and butyrate) and one material reuse (AC reuse) constitutes a valuable upgrading approach for this yet unexploited waste biomass.