Brazil is a global leader in the orange industry, producing approximately one-fourth of the world’s oranges and generating over 50% of the associated waste. These by-products are rich in bioactive compounds; however, their improper disposal poses environmental risks. This study employs an eco-friendly approach—microwave-assisted extraction—to recover valuable compounds from orange juice production waste. The extracted compounds were analyzed using nuclear magnetic resonance (NMR) and gas chromatography–mass spectrometry (GC–MS). Key bioactives, including D-limonene, valencene, hesperidin, and carbohydrates, were successfully identified. NMR effectively traces and semi-quantifies these compounds, while microwave-assisted extraction enables the sustainable recovery of high-purity hesperidin, confirmed by NMR (87.66%) and HPLC (84.30%) analyses.