Poly(ether ether ketone) (PEEK) is a high-performance, semicrystalline thermoplastic that has attracted significant interest for material extrusion additive manufacturing techniques such as fused filament fabrication (FFF) but remains beset by poor weld strength. Here, it is observed that under typical processing conditions that surface crystallization prevents effective weld formation between printed layers, leading to weak and brittle welds. Utilizing atomic force microscopy, differential scanning calorimetry, bulk tensile fracture testing, and mode III tear testing, appropriate processing conditions and post-print annealing conditions have been developed to improve the weld strength of FFF-PEEK. After printing PEEK in an amorphous state through careful control of the thermal gradients during printing a two-step annealing procedure yields crystalline PEEK welds that are 6–8 times stronger than welds in FFF-PEEK that crystallized during printing. • Fused filament fabrication of PEEK leads to weak and brittle welds with printed fibers. • Atomic force microscopy is used to map the weld microstructure of PEEK and is correlated with measurements of weld strength. • Interfacial crystallization between fibers inhibits weld formation, reducing the strength of fused filament fabricated PEEK. • A printing and annealing procedure reduces interfacial crystallization, improving PEEK weld strength from 7 MPa to 37 MPa.