Automated manufacturing techniques, such as Automated Fiber Placement (AFP), offer an opportunity over conventional manufacturing methods, such as autoclave curing, to save time and expenses. The present research focuses on evaluating the Interlaminar Shear Strength (ILSS) of Carbon/PEEK thermoplastic composite laminates manufactured by AFP in-situ consolidation and autoclave re-consolidation using the Short-Beam Shear (SBS) test. Additionally, a methodology is proposed to capture the differences observed in ILSS using a finite element simulation. In this respect, a thermoplastic laminate was fabricated using AFP in-situ consolidation. Baseline laminate was also produced by re-consolidating another AFP-made laminate inside the autoclave. A micrographic study was conducted to investigate the void content and fiber distribution resulting from each manufacturing process. The test results showed that the AFP technique results in an ILSS of the laminate that is 37 % lower than that of the autoclave-reconsolidated laminate. The distinct mechanical behaviour in the SBS test arising from in-situ consolidation and autoclave re-consolidation was differentiated in the finite element modeling utilizing cohesive elements. This distinction was achieved by numerically finding the proper interface strength properties based on the SBS experimental results. These interface properties serve as valuable input parameters for conducting further finite element modeling and analyses of Carbon/PEEK thermoplastic composite laminates manufactured by AFP in-situ consolidation.