This study aims to assess the influence of peel-ply (PP), mechanical abrasion (MA), and atmospheric plasma activation (APA) treatments on Mode-I and Mode-II fracture toughness of carbon fiber/ poly-ether-ketone-ketone (CF/PEKK) composite joints. A comprehensive examination of the topography and wettability of the adherend surfaces is conducted using various methods. The CF/PEKK adherends are produced through an automated fiber placement (AFP) process, and the CF/PEKK bonded joints are prepared using two different structural adhesive films, one of which has a lower strength, while the other has a higher strength. To evaluate their fracture toughness properties, double cantilever beam (DCB) and end-notched flexure (ENF) tests are carried out in accordance with ASTM standards. Acoustic emission sensors are used to monitor the test specimens during DCB tests, allowing for an in-depth evaluation of the failure modes and damage propagations in the joints. The results show that the GIC and GIIC values of the APA-treated CF/PEKK bonded joints are remarkably higher than those of the untreated ones, with a range of improvement of 34.0–84.8 times and 7.5–17.4 times, respectively. Adhesive failure is the dominant failure mode on the surfaces of non-treated (NT) and PP samples, while cohesive failure is more prominent in those treated with MA and APA. The failure modes of the treated samples varied depending on the adhesive used, with APA-treated samples always exhibiting a cohesive failure. It is observed that the AE counts increase more slowly in APA-treated samples compared to MA-treated joints as delamination progresses more slowly with cohesive failure dominant, which leads to a lower release of AE energy.