Due to the semi-crystalline structure of native starch granules, enzymatic modification of these solid, raw, entities by branching enzyme (BE) is limited. Here, we describe a method to efficiently modify starch by BE after maltogenic α-amylases pre-treatment. This pre-treatment produced pores at the starch granule surface, which decreased the granular yield, but increased the branching degree in starch molecules. BE post-treatments recovered the yield, increased the content of long amylose chains, and the starch crystallinity. WAXS analysis showed that BE transformed the unresolved doublet peak at 2θ 17° and 18° to a strong peak at 2θ 17°, i.e. transformed the granules from the A-type to a mixed A-, B-type allomorph. Syneresis of starch gels increased with increasing BE concentrations and increased the content of slowly digested starch in retrograded starch preparations. Rheology data demonstrated that low and medium BE concentrations produced starch gels with higher G′ and G″ after storage for 1day, whereas high BE concentrations reduced both G′ and G’’. Our data demonstrate the potential of clean, enzyme-based protocols using sequential addition of starch active enzymes for post-harvest modification of raw starch granules to obtain clean and functional starch.