In this work, we develop a mathematical framework for a selected configuration interaction (SCI) algorithm within a bi-orthogonal basis for transcorrelated (TC) calculations. The bi-orthogonal basis used here serves as the equivalent of the standard Hartree–Fock (HF) orbitals. However, within the context of TC, it leads to distinct orbitals for the left and right vectors. Our findings indicate that the use of such a bi-orthogonal basis allows for a proper definition of the frozen core approximation. In contrast, the use of HF orbitals results in bad error cancellations for ionization potentials and atomization energies (AE). Compared to HF orbitals, the optimized bi-orthogonal basis significantly reduces the positive part of the second-order energy (PT2), thereby facilitating the use of standard extrapolation techniques of hermitian SCI. While we did not observe a significant improvement in the convergence of the SCI algorithm, this is largely due to the use in this work of a simple three-body correlation factor introduced in a recent study. This correlation factor, which depends only on atomic parameters, eliminates the need for re-optimization of the correlation factor for molecular systems, making its use straightforward and user-friendly. Despite the simplicity of this correlation factor, we were able to achieve accurate results on the AE of a series of 14 molecules on a triple-zeta basis. We also successfully broke a double bond until the full dissociation limit while maintaining the size consistency property. This work thus demonstrates the potential of the BiO-TC-SCI approach in handling complex molecular systems.