Background and objective L-methioninase has attracted much attention with respect to its proposed applications in both pharmaceuticals and food industry. The aim of this study was to develop an economic medium formulation using agro-industrial by-products as substrates for large-scale production of L-methioninase. Materials and methods Identification of a high L-methioninase-producing yeast isolate was carried out using 18S rRNA molecular technique. Screening of various agro-industrial by-products and optimization of different process parameters were investigated. Partial purification and characterization of a crude enzyme were carried out. Results and discussion A high L-methioninase-producing yeast isolate was phylogenetically identified as Wickerhamomyces subpelliculosus. Among different agro-industrial by-products tested, orange pulp supported maximum enzyme production (94.08 U/ml) followed by cane and beet molasses. In addition, corn steep liquor (CSL) gave high enzyme level (141.12 U/ml) and could be used as an inexpensive alternate for yeast extract. The optimum growth conditions were found to be orange pulp 30% (w/v), CSL 4% (v/v), CaCl2 0.05%, and KH2PO4 0.05% (w/v) at pH 6.0 after 48 h of incubation. This developed medium formulation increased L-methioninase production (161.95 U/ml) by twofold compared with that obtained by the Czapek–Dox’s medium (73.92 U/ml). Crude enzyme was partially purified by heat treatment at 70°C with 2.9 purification fold. The enzyme activity was optimal at temperature 60°C and pH 7.0. The results showed that a mixed formulation of orange pulp and CSL can be used as an effective and economic substrate for the production of L-methioninase by W. subpelliculosus.