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Extrusion is a widely used technique for cereal processing which combined with enzymatic action could offer extended possibilities for obtaining clean label modified flours. In this study, native and extruded maize flours were subjected to a branching enzyme (B) and a synergetic branching enzyme and maltogenic a-amylase (BMA) treatments in order to modulate their hydrolysis properties. The microstructure, pasting properties, <i>in vitro </i>starch hydrolysis and resistant starch content of flours were assessed. Starch granules were loosed from native flour particles during B and BMA treatments. However, only extruded flours displayed a much higher reactivity towards enzymes as seen by the increase of the roughness and the cavities in the surface of the particles. A reduction in the setback was observed for B and BMA native flours, in opposition to the flat pasting profile of their extruded counterparts. Regarding starch hydrolysis, extruded samples presented higher hydrolysis rates at the early stage than their native counterparts. The glucose release increased gradually for native flours with the time of reaction, whereas for extruded flours a fast glucose release was observed during the first minutes of reaction. However, the susceptibility of native and extruded flour to the pancreatic a-amylase hydrolysis did not change with any of the enzyme treatments, as the final asymptote and the digestion rate constant indicated. After 16 hours of hydrolysis, resistant starch content was lower for treated extruded samples. Results suggested that the negative effect of rapid starch digestion induced by extrusion could not be overcome by increasing the branching points and the proportion of short chains in treated extruded samples. This study shows that changes produced at larger hierarchical levels in the starch structure could mask changes produced in the primary starch structure