Hazelnut (HS) and walnut (WS) shells, an abundant by-product of the processing industries of these edible nuts, are traditionally considered as a low-value waste. However, they are a source of valuable compounds with an interesting chemical profile for the chemical and pharmaceutical sectors. In this study, the lipophilic and hydrophilic extracts present in HS and WS were quantified and identified, then the polar fractions were chromatographically separated, and their antioxidant capacity was studied. The experimental work includes the isolation of crude lipophilic and hydrophilic extracts by an accelerated extraction process, chromatographic analysis (gas chromatography-flame ionization (GC-FID), GC-mass spectroscopy (GC-MS), high-performance size-exclusion chromatography (HPSEC), thin-layer chromatography (TLC)), and quantification of the components. In addition, a thorough compositional characterization of the subgroups obtained by flash chromatography and their antioxidant capacity was carried out. The gravimetric concentrations showed different lipophilic/hydrophilic ratios (0.70 for HS and 0.23 for WS), indicating a higher proportion of polar compounds in WS than in HS. Moreover, the lipophilic extracts were principally composed of short-chain fatty acids (stearic, palmitic, and oleic acid), triglycerides, and sterols. The polar fractions were screened by thin-layer chromatography and then separated by flash chromatography, obtaining fractions free of fatty acids and sugar derivatives (97:3 in HS and 95:5 in WS), and mixtures richer in phenolic compounds and flavonoids such as guaiacyl derivatives, quercetin, pinobanksin, and catechin. The most polar fractions presented a higher antioxidant capacity than that of the crude extracts.