This work aims at designing functional biomaterials through selective chemical modification of xylan from beechwood. Acidic hydrolysis of xylan led to well-defined oligomers with an average of six xylose units per chain and with an aldehyde group at the reductive end. Reductive amination was performed on this aldehyde end group to introduce an azide reactive group. "Click chemistry" was then applied to couple these hydrophilic xylans moieties with different hydrophobic fatty acid methyl esters that were previously functionalized with complementary alkyne functions. The resulting amphiphilic bio-based conjugates were then self-assembled using three different methods, namely, direct solubilization, thin-film rehydration/extrusion, and microfluidics. Well-defined micelles and vesicles were obtained, and their high loading capacity with propiconazole as an antifungal active molecule was shown. The resulting vesicles loaded with propiconazole in a microfluidic process proved to significantly improve the antifungal activity of propiconazole, demonstrating the high potential of such xylan-based amphiphiles.