Producing chestnut flour from chestnuts that fail to meet commercial calibre standards offers a dual opportunity: it valorises an otherwise discarded fraction of the harvest and enables whole-fruit processing without peeling and shell-separation, reducing processing steps and costs. This work investigates a shell-enriched chestnut flour obtained from non-marketable chestnuts cooked with thermal water, incorporating both the pericarp and pellicle. Cooking was selected for its documented capacity to reduce antinutritional compounds such as tannins via leaching and thermal degradation, as shown for other tannin-rich foods including lupin beans. Kernel and shell fractions were characterised separately, raw and after cooking in tap water and in two thermal waters (Chaves and Ourense), to establish the compositional basis for the flour formulation. Cooking with Chaves thermal water significantly increased kernel fibre content (10.75 ± 0.21 g/100 g DW) relative to raw (9.82 ± 0.26) and tap-water-cooked samples (10.32 ± 0.13; p < 0.05), whilst significantly reducing lipid content (2.16 ± 0.04 vs. 3.17 ± 0.05 g/100 g DW; p < 0.05). Shell protein content was also significantly higher after Chaves cooking (5.21 ± 0.18 g/100 g DW) than under any other condition (p < 0.05). Shell fibre remained within a comparable range across conditions (61–69 g/100 g DW) but was significantly reduced after thermal-water cooking relative to raw and tap-water samples (p < 0.05). The shell-enriched flour formulation (85% kernel, 15% shell) reflects the natural shell proportion rather than an arbitrary fortification level. Its theoretical composition across processing conditions was: moisture 4.87–9.62, protein 5.70–7.44, fat 1.97–2.78, dietary fibre 17.95–19.08, and ash 1.78–1.98 g/100 g DW. Resistant starch and antinutrient content — both expected to benefit from cooking — remain under analysis and will be presented at the conference. These findings support whole-fruit processing with thermal-water cooking as a sustainable strategy to improve nutritional quality and value while reducing waste.