Protein-based microfibers have potential applications in bioengineering and food but preserving and utilizing the unique nanomechanical properties of their protein building blocks at the micrometer scale remains a challenge. This study investigates the bottom-up fabrication of core-shell fibers by coaxial microfluidic spinning of pectin and β-lactoglobulin in different conformational states (monomeric, amyloid fibrils, shortened amyloid fibrils in their isotropic/nematic phases), gelled in CaCl₂ solution. Fiber diameters ranged between 478 and 855 μm (wet state) and 107-135 μm (dry state). They showed clear core-shell cross-sections, except pectin-β-lactoglobulin monomer fibers where the compact protein is presumably understood to diffuse through the pectin matrix. The molecular orientation of the fiber building blocks was expressed as order parameters representing the alignment of pectin chains and amyloid fibrils parallel to the fiber axis calculated from synchrotron wide-angle X-ray scattering (WAXS) with a spatial resolution of 20 μm. Introduction of amyloid fibrils as the protein core increased the Young's modulus from 3.3 to 6.4 GPa and tensile strength from 117 to 182 MPa compared to pure pectin fibers. Increasing the protein core flow rate from 1 to 2 mL/h, however, caused helical bending of the core jet, a decrease in order, and ultimately worsened mechanical performance. Overall, full length amyloid fibrils proved to be more beneficial to the mechanical properties than shortened amyloid fibrils. By providing insight into the relationship between protein conformation, spinning flow rate, and resulting mechanical properties of core-shell microfibers, these results may contribute to the field of novel fibrous protein-based materials.