Numerous missions leverage the weak stability boundary in the Earth–Moon–Sun system to achieve a safe and cost-effective access to the lunar environment. These transfers are envisaged to play a significant role in upcoming missions. This paper proposes a novel method to design low-energy transfers by combining the recent Theory of Functional Connections with a homotopic continuation approach. Planar patched transfer legs within the Earth–Moon and Sun–Earth systems are continued into higher-fidelity models. Eventually, the full Earth–Moon transfer is adjusted to conform to the dynamics of the planar Earth–Moon Sun-perturbed, bi-circular restricted four-body problem. The novelty lies in the avoidance of any propagation during the continuation process and final convergence. This formulation is beneficial when an extensive grid search is performed, automatically generating over 2000 low-energy transfers. Subsequently, these are optimized through a standard direct transcription and multiple shooting algorithm. This work illustrates that two-impulse low-energy transfers modeled in chaotic dynamic environments can be effectively formulated in Theory of Functional Connections, hence simplifying their overall design process. Moreover, its synergy with a homotopic continuation approach is demonstrated.