Abstract This paper presents the immobilization of the Thermoanaerobacter cyclomaltodextrin glucanotransferase (CGTase) enzyme into cross-linked 6% agarose beads activated by high density of linear aldehyde groups (glyoxyl-agarose) that allow the establishment of multi-attachment enzyme-support bonds. The immobilization conditions were 25 °C, pH 10 and 5 h of contact time. The immobilization yield was almost 100% and the activity recovery was ca. 32%. The biocatalyst at 85 °C was capable of producing cyclodextrins (CDs) from dextrin or soluble starch (both at 1% (w/v)) at a greater rate than the soluble enzyme. In addition, the biocatalyst maintained 90% of its initial activity after 5 h at 85 °C. The maximum conversion of dextrin to β-CD and γ-CD (total mass of produced CDs/substrate initial mass × 100) was 29% both for the soluble and immobilized enzymes. Using starch as substrate the maximum starch conversion to β-CD and γ-CD was 29% and 38%, for the immobilized and soluble enzyme, respectively. The β-CD selectivity yield [mass of β-CD produced/(mass of β-CD produced + mass of γ-CD produced) × 100] increased from 67.9% for the free enzyme to 85.4% for the immobilized CGTase.