Investigations concerning recombinant α-amylases from Pyrococcus woesei and thermostable α-glucosidase from Thermus thermophilus indicate their suitability for starch processing. Furthermore, the study of recombinant β-galactosidase from Pyrococcus woesei suitable for purpose of low lactose milk and whey production are also presented. The activity of this enzyme in a wide pH range of 4.3–6.6 and high thermostability suggests that it can be used for processing of dairy products at temperatures which restrict microbial growth during a long operating time of continuous-flow reactor with an immobilized enzyme system. Preparation of recombinant α-amylase and β-galactosidase was facilitated by cloning and expression of genes from Pyrococcus woesei in Escherichia coli host. Satisfactory level of recombinant enzymes purification was achieved by thermal precipitation of native proteins originated from Escherichia coli. The obtained α-amylase has maximal activity at pH 5.6 and 93°C. The half-life of this preparation (pH 5.6) at 90°C and 110°C was 11 h and 3.5 h, respectively, and retained 24% of residual activity following incubation for 2 h at 120°C. An advantageous attribute of recombinant α -amylase is independence of its activity and stability on calcium salt. α-Glucosidase from Thermus thermophilus also not require metal ions for stability and retained about 80% of maximal activity at pH range 5.8–6.9. Thus, this enzyme can be used together with recombinant α-amylase.