The expanding citrus industry in Morocco generates large volumes of underutilized by-products and sorting rejects. Rich in fermentable sugars and bioactive compounds, these residues offer potential for biotechnological conversion. This study focused on valorizing citrus sorting rejects by isolating native microorganisms for bioethanol and acetic acid production. Juices from sorting rejects of four citrus varieties were used as fermentation substrates. Yeast and acetic acid bacteria were isolated from Moroccan sourdough and traditional vinegars, then screened for fermentation efficiency. Yeast strain L4 and acetic acid bacteria strain AV22 showed superior performance compared to a commercial Saccharomyces cerevisiae strain. L4 produced 4.03% (v/v) ethanol from Sanguinelli juice without sucrose, and 11.4% with added sucrose. The fermented must yielded 8.40 L of vinegar containing 5.56% (w/v) acetic acid in a 10 L bioreactor, and was successfully scaled up to 80 L of vinegar with 7.0% (w/v) acidity in a 500 L pilot-scale acetifier. Sensory evaluation by 51 untrained panelists confirmed the vinegar’s high acceptability. This work demonstrates the potential of indigenous strains in converting citrus waste into value-added products, promoting sustainable waste management and circular bioeconomy practices. Future research will focus on process optimization, scaling up, and co-product recovery to improve economic feasibility.