AbstractCollagen (Col) composite fibers containing various functionalized multiwalled carbon nanotubes (MWNTs) were prepared via microfluidic spinning, and the influences of MWNT content and type on the performances of the composite fibers were investigated by transmission electron microscope, UV–vis, SEM, Fourier Transform Infrared Spectrometer, differential scanning calorimetry, X‐ray diffraction, and tensile testing. The Col composite fibers showed tightly packed bundle structures on surfaces originated from the high shear rates in the microfluidic channels, and MWNT facilitates the self‐assembly of Col molecules, leading to the ordered arrangement of Col fibrils along the fiber axis. When the loading of carboxylated MWNT (cMWNT) was 0.5 wt%, the tensile strength of Col/cMWNT achieved the maximum of 1.94 cN/dtex owing to the excellent hydrogen bond and electrostatic interactions between the carboxyl groups in cMWNT and amino groups in Col molecules, which is significantly higher than those composite fibers made from unfunctionalized and hydroxylated MWNT. Moreover, with the incorporation of MWNT the thermal stability and water resistance of Col fibers were improved due to the enhanced interfacial interactions between Col and MWNT. The fabrication method in this work enables the controlled formation of Col fibers and demonstrates huge potential for use in Col‐based biomaterials.Highlights Novel collagen (Col)/multiwalled carbon nanotube (MWNT) composite fibers were prepared via microfluidic spinning. The Col composite fibers showed tightly packed bundle surface structures. Col/carboxylated MWNT achieved the maximum tensile strength of 1.94 cN/dtex. MWNT enhanced thermal stability and water resistance of Col fibers.