Agro-industrial wastes are potential starting materials for the production of useful value-added compounds, including prebiotic oligosaccharides. In this paper, we evaluated the potential of thermophilic bacterial pectin- and xylan-degrading recombinant enzymes for the degradation of the agro-industrial wastes: apple pomace, wheat straw, wheat bran and distillers grains. For the immobilization of pectate lyase and xylanase, three different supports were used. The effect of enzyme immobilization was analyzed in terms of enhanced thermostability and activity against these wastes. For xylanase, the highest thermostability was achieved by immobilization on Sepabeads EC-EP/M. The best activity against bran and grains was obtained by immobilization on Sepabeads EC-HA/M. For pectate lyase, the highest thermostability was achieved by immobilization on Sepabeads EC-EP/M, however, activity against apple pomace pectin was slightly reduced by this immobilization. The length of oligosaccharides produced by both free and immobilized enzymes was also determined.