This paper documents an investigation of the effects of fibre treatment on New Zealand flax (harakeke) fibre reinforced polylactic acid (PLA) composites. The raw fibre was alkali digested, followed by bleaching and then modified with ultrasonication. Alkali treatment removed lignin and other non-cellulosic components and partially separated fibre bundles while bleaching further removed lignin and improved the separation of elementary fibres, resulting in microfibres with a cellulose content 92 wt%. With subsequent ultrasonication, microfibrils could be seen partially separated (defibrillation) at fibre surfaces. Treated fibres were compounded with PLA at a fibre loading of 30 wt% and extruded into composite filaments. Filaments from alkali, bleached and ultrasonication-treated fibres had smooth surfaces, which translated into high-quality printability along with good mechanical performance. The combination of chemically treated microfibres with selective surface defibrillation using ultrasonication and fibre alignment induced by the printing process resulted in 3D printed samples with a tensile strength of 79 MPa and Young’s modulus of 8.7 GPa, which are the highest values reported so far for 3D printed PLA-based composites reinforced with short fibres.