The accurate, robust, and efficient prediction of transition in viscous flows is a significant challenge in computational fluid dynamics. We present a coupled high-fidelity iterative approach that leverages the FUN3D flow solver and the LASTRAC stability code to predict transition in low-disturbance environments, initiated by the linear growth of boundary-layer instability modes. Our method integrates the ability of FUN3D to compute mixed laminar–transitional–turbulent mean flows via transition-sensitized Reynolds-Averaged Navier–Stokes equations with the ability of LASTRAC to perform linear stability analysis, all within an automated framework that requires no intermediate user involvement. Unlike conventional frameworks that rely on classical stability theory or reduced-order metamodels, our approach employs parabolized stability equations to provide more accurate and reliable estimates of disturbance growth for multiple instability mechanisms, including Tollmien–Schlichting, Kelvin–Helmholtz, and crossflow modes. By accounting for the effects of mean-flow nonparallelism as well as the surface curvature, this approach lays the foundation for improved N-factor correlations for transition onset prediction in a broad class of flows. We apply this method to three distinct flow configurations: (1) flow over a zero-pressure-gradient flat plate, (2) the NLF-0416 airfoil with both natural and separation-induced transition, and (3) a 6:1 prolate spheroid, where transition is primarily driven by crossflow instability. For two-dimensional cases, a formulated intermittency distribution is used to model the transition zone between the laminar and fully turbulent flows. The results include comparisons with experimental measurements, similar numerical approaches, and transport-equation-based models, demonstrating good agreement in surface pressure coefficients, transition onset locations, and skin-friction coefficients for all three configurations. In addition to contributing a couple of new insights into boundary-layer transition in these canonical cases, this study presents a powerful tool for transition modeling in both research and design applications in aerodynamics.