This research aims to vary functional properties of native and extruded wheat flours combining cyclodextrin glucanotransferase and extrusion treatments. The level of released cyclodextrins (CD) was assessed, besides the microstructure, crystallinity, pasting properties and starch hydrolysis of the flours. Photomicrographs of enzymatically treated flours suggested the production of fragile structures that broke easily. Enzymatic hydrolysis was significantly higher in extruded flours, as confirmed the CD levels, being predominant the γ-CD followed by α-CD, whereas very low β-CD values were obtained probably due to the formation of CD-lipid complexes, as suggested X-ray diffractometry results. Both extruded and native samples showed very low viscosity and flat pasting profile consequence of the enzyme hydrolytic activity on the starch chains. Enzymatically treated flours (native and extruded) showed higher hydrolysis rates at the early hydrolysis stage, and extruded flours exhibited higher fractal exponent h in agreement with the extended crystalline structures resulting from enzymatic treatment.