Abstract Increasing interest in 3D-printed high-performance polymers is observed due to their excellent mechanical properties and high resistance to chemical and thermal degradation. One of the ongoing challenges is to achieve sufficient joint strength because of the inertness of thermoplastics. In the current work, effects of surface treatment on shear bond strength of 3D-printed samples were focused and assessed. First, polyetherimide (PEI), polyether ether ketone (PEEK) and PEEK/CF(carbon fiber) as adherend were produced via FDM 3D printing. Then, sanding or atmospheric plasma treatments were carried out to improve the surface wettability of the 3D-printed specimens. Significantly, reduction in surface roughness was observed in sanding treated specimens, while nearly no change occurred in plasma-treated counterparts. However, surface free energy and wettability were greatly improved after plasma treatment. Single lap-shear tests and failure mode for PEI, PEEK and PEEK/CF using two different adhesives (film and liquid) were investigated, and the effect of surface treatment on bond strength was further compared. Results suggested that liquid adhesive contributed higher joint strength for surface-treated specimens in comparison to film adhesive. Besides, atmospheric plasma treatment is more efficient and safer method for 3D-printed PEEK and PEEK/CF, achieving a higher joining strength.