Incorporation of agriculture unused by-products into materials is a significant strategy to develop sustainable and profitable biobased products while limiting environmental impacts of plastics. In addition, the design of such biomaterials by 3D printing techniques as fused deposition modelling (FDM) can bring new functionalities. However, the plant material properties and the interactions with the polymeric network are critical to control during the process, from filament production to 3D printing, to obtain a high-quality material. In this work, flax shives was selected as the starting plant by-product. Indeed, flax provides high-quality fibers for composite materials but their shives, which are the plant woody core removed during flax processing, have few applications despite their very low cost and large availability. So flax shives were first selectively milled to be grafted to a fluorophore whose fluorescence varies under pH. The resulting fluorescent shives were processed with poly-(butylene-terephthalate) (PBAT) by extrusion to produce a filament reinforced with 10%-wt of flax shives (whose 10% were grafted). Then this filament was 3D printed to produced different specimens with complex shapes. Extensive microstructural characterization (particle size and shape analysis, X-ray microtomography) demonstrated that flax particles are homogeneously distributed into the 3D printed material. Also, despite the relatively low content of fluorescent flax shives in the final 3D printed material (1%-wt) and successive heating stages (during extrusion and 3D printing), a strong fluorescent emission could still be measured. This work paves the way for using flax shives and other plant by-products as reinforcements into composites while conferring them fluorescent properties, thus making 4D materials with potential applications as sensors depending on the fluorophore selected.