Generation of cyanide-containing wastewater is a growing problem worldwide as numerous cyanide complexes are highly unstable and degrade to form free cyanide (F-CN), the most toxic form of cyanide. Agro-waste materials, such as sweet orange (Citrus sinensis) waste from the citrus industry, are rich in readily metabolisable carbohydrates that can supplement microbial activity and thus support biodegradation of toxic compounds in wastewater. This study reports on optimal operating conditions for the continuous biodegradation of F-CN in wastewater using an Aspergillus awamori isolate in a process supported solely using C. sinensis waste extract. The optimal degradation conditions were pH 8.75 and 37.02 °C with the isolate's F-CN tolerance being observed up to 430 mg F-CN/L. Furthermore, the ammonium produced as a by-product of F-CN degradation was also metabolised by the A. awamori, with negligible residual citric acid and formate being observed in the effluent post treatment. This study demonstrates the feasibility of using agricultural waste as a primary and sole carbon source for the cultivation of a cyanide-degrading A. awamori species for F-CN degradation under alkaline conditions.