The aim of this work is to study the effect of high-temperature compaction (HTC) upon the polymorphism and the mechanical behavior of an additively manufactured (AM) carbon fiber-reinforced polyamide (PA6). Different pressure and temperature levels during HTC were tested to determine the overall effect on the mechanical behavior and material crystalline composition. Treated, carbon fiber-reinforced PA6 samples were analyzed using differential scanning calorimetry, X-ray diffraction, thermogravimetric analysis, scanning electron microscopy, and three-point bending testing. When considered with respect to as-printed samples, an HTC temperature of 190 °C combined with 80 psi pressure resulted in an increased flexural modulus and strength of 47% and 58%, respectively. This increase was attributed to the decrease in AM-induced cracking, voids (both inside and between the beads), and crystalline solid-state transition in the PA6. The effect of pressure and temperature on the crystalline structure was discussed in terms of an increased degree of crystallinity and the amount of α-phase. Therefore, HTC can help overcome some limitations of traditional annealing, which can result in recrystallization-induced cracking which can lead to material embrittlement. The proposed HTC method demonstrates the potential in improving the mechanical behavior of AM thermoplastic composites.