Here, we propose the utilization of atmospheric plasma activation (APA), which outperforms peel-ply (PP) treatment and mechanical abrasion (MA) in achieving high-performance adhesively bonded carbon fiber/polyetherketoneketone (CF/PEKK) composites. This study covers several key aspects, including the chemical and morphological characterization of treated surfaces and mechanical performance assessments of single lap-joints (SLJs) under tensile and flexural loading conditions. In addition, in-situ acoustic emission (AE) monitoring is employed during tensile tests to determine dominant damage types and failure modes in the SLJs. Surface analysis shows that MA increases roughness, PP treatment decreases wettability, while APA enhances wettability by modifying the surface chemistry. Tensile and flexural tests reveal that APA-treated joints surpassed non-treated (NT) ones, with up to 5- and 7-times higher load-carrying performance, respectively, while fracture analysis suggests a shift from adhesive to cohesive failure. AE results show that increased AE events related to cohesive failure align with improved interface interactions.