Understanding the fine details of self-assembly of building blocks into complex hierarchical structures represents a major challenge en route to the design and preparation of soft matter materials with specific properties. Enzymatically-synthesised cellodextrins are known to have limited water solubility beyond DP9, a point at which they self-assemble into particles resembling the anti-parallel cellulose II crystalline packing. We have prepared and characterized a series of site-selectively fluorinated cellodextrins of different degrees of fluorination and substitution patterns by chemoenzymatic synthesis. The structural characterization of these materials at different length scales, combining advanced NMR and microscopy methods, showed that multiply 6-fluorinated cellodextrin chains assembled into particles presenting morphological and crystallinity features that are unprecedented for cellulose-like materials. In contrast, the introduction of a single fluorine atom per cellodextrin chain had a minor impact on materials structure. Our work emphasizes the strength of combining chemoenzymatic synthesis, fluorinated building blocks and advanced NMR and microscopy methods for the thorough characterization of hierarchical structures, leading to the controlled design of new biomaterials with specific properties.