<p>Interlayer adhesion remains a primary limitation in material extrusion additive manufacturing (MEX-AM), where the bonding strength depends on the complex thermo-mechanical interactions arising during strand-on-strand deposition. This work presents a three-dimensional CFD framework of interlayer adhesion, together with dynamic strand-on-strand interface tracking and analysis of bottom-layer deformation. Validated across a wide range of process conditions the proposed model consistently outperforms existing semi-analytical approaches, particularly under low temperatures and high flow rates. A parametric study based on dimensionless kinematic (V/U), geometric (G/D), and thermal (T/T_g) ratios was conducted under natural and forced convection (HTC = 50–150 W m⁻²&#xa0;K⁻¹) and different layer cooling times (0.5–2.0&#xa0;s). Increasing T/T_g from 2.25 to 2.75 raised penetration length by 50% under short cooling times, while lowest values of G/D induced bottom-layer deformation up to 58%. Accordingly, a physically grounded metric is proposed to guide process parameter selection toward improved wetting conditions while limiting bottom-layer deformation, finding distinct optima at V/U = 1 and G/D = 0.50. High extrusion temperatures coupled with forced convection maximizes wetting while reducing deformation by an order of magnitude. The proposed framework provides practical manufacturing guidelines and advances physics-based digital twins for improving interlayer bonding conditions in MEX-AM components.</p>