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Background  The recycling of agro-industrial wastes is at present limited by the availability of efficient and low-cost enzyme cocktails. The use of these materials as culture media to produce the enzymes can contribute to the profitability of the recycling process and to the circular economy. The aim of this work is the construction of a recombinant yeast strain efficient to grow in mixed whey (residue of cheese making) and beet molasses (residue of sugar manufacture) as culture medium, and to produce heterologous α-galactosidase, an enzyme with varied industrial applications and wide market.    Results  The gene  MEL1 , encoding the α-galactosidase of  Saccharomyces cerevisiae , was integrated (four copies) in the  LAC4  locus of the  Kluyveromyces lactis  industrial strain GG799. The constructed recombinant strain produces high levels of extracellular α-galactosidase under the control of the  LAC4  promoter, inducible by lactose and galactose, and the native  MEL1  secretion signal peptide.  K. lactis  produces natively beta-galactosidase and invertase thus metabolizing the sugars of whey and molasses. A culture medium based on whey and molasses was statistically optimized, and then the cultures scaled-up at laboratory level, thus obtaining 19 U/mL of heterologous α-galactosidase with a productivity of 0.158 U/L h, which is the highest value reported hitherto from a cheap waste-based medium.    Conclusions  A  K. lactis  recombinant strain was constructed and a sustainable culture medium, based on a mixture of cheese whey and beet molasses, was optimized for high productivity of  S. cerevisiae  α-galactosidase, thus contributing to the circular economy by producing a heterologous enzyme from two agro-industrial wastes.    Electronic supplementary material  The online version of this article (10.1186/s12934-018-0988-6) contains supplementary material, which is available to authorized users.

Valuation of agro-industrial wastes as substrates for heterologous production of α-galactosidase