Apple industrial by-products are a promising source of bioactive compounds with direct implications on human health. The main goal of the present work was to characterize the Jonathan and Golden Delicious by-products from their fatty acid, amino acid, and volatile aroma compounds’ point of view. GC-MS (gas chromatography-mass spectrometry) and ITEX/GC-MS methods were used for the by-products characterization. Linoleic and oleic were the main fatty acids identified in all samples, while stearic acid was the representant of saturated ones. With respect to amino acids, from the essential group, isoleucine was the majority compound identified in JS (Jonathan skin) and GS (Golden skin) samples, lysine was the representant of JP (Jonathan pomace), and valine was mainly identified in GP (Golden pomace). A total number of 47 aroma volatile compounds were quantified in all samples, from which the esters groups ranged from 41.55–53.29%, aldehydes 29.75–43.99%, alcohols from 4.15 to 6.37%, ketones 4.14–5.72%, and the terpenes and terpenoids group reached values between 2.27% and 4.61%. Moreover, the by-products were valorized in biscuits manufacturing, highlighting their importance in enhancing the volatile aroma compounds, color, and sensorial analysis of the final baked goods.