Automated fiber placement (AFP) provides an efficient route for manufacturing thermoplastic composite laminates. However, in-situ consolidation remains constrained by a limited effective thermal history and rapid cooling, thereby limiting interfacial healing, crystallization development, and interlaminar quality. Here, we propose an in-mold annealing (IMA) strategy for AFP-fabricated carbon fiber reinforced low-melt poly (aryl ether ketone) (CF/LM-PAEK) laminates. IMA is a mold-constrained post-AFP thermal treatment designed to extend the effective thermal history of the laminate without demolding. We systematically investigate the effects of tool temperature and subsequent IMA on the consolidation quality and performance of AFP-fabricated laminates. The optimal IMA condition was identified as 250 °C for 3 h. Under this condition, the void content was reduced to 0.387%, and the DSC crystallinity increased to 34.91%. Consequently, the ILSS and flexural strength reached 91.29 MPa and 1355.11 MPa, corresponding to 90.5% and 95.4% of the thermoformed reference, respectively. These results indicate that IMA promotes post-AFP void reduction, further crystallization, and improved interlaminar structural continuity. It provides a practical route to improve laminate quality while keeping the laminate on the same tool after AFP.