Exploitation of residual citrus biomass in biorefineries should include extraction of bioactive compounds, with particular attention to the high extractable content of this by-product. In fact, according to the principles of biorefinery, transforming “waste” to “secondary raw material” can totally or partially reduce the economic and ecological issues. In this study, green residual biomass from citrus trees located in a Capbon peninsula region (Tunisia) was analyzed. A phytochemical study was carried out by determining the content of polyphenols and flavonoids and antioxidant activities. Gas chromatography coupled with time-of-flight mass spectrometry (GC-TOFMS) analysis allowed the identification and evaluation of bioactive compounds as quinic acid, proline, alpha-linolenic acid and alpha-amyrin known for their wide range of applications. In addition, the fragrant aroma composition of petitgrain essential oil displayed substantial qualitative and quantitative differences that could serve as a promising natural source used in the development and formulation of functional foods and pharmaceutical products, in flavoring, liqueurs, perfumes, and medicines of ingredients. Then, the hydrodistillation effluent was assessed for its antioxidant and antifungal potential from where it is proven that it could be a source of the bioactive compounds with high spectrum of biological activities. From the point of view of the integral valorization of these underexploited and wasted bioresidues offers the double opportunity to recover biosourced molecules with high added value on the one hand and to reduce the pollutant effects on the other hand, and thus, contributing to promoting sustainable development and bioeconomy via a zero waste integrated approach priming the green biorefineries pathways.