This paper introduces a new adaptation of the enthalpic lattice Boltzmann method (LBM) tailored to simulate the intricate dynamics of conjugate heat transfer in non-homogeneous media, showcasing considerable potential for enhancing heat exchanger designs. This approach expands upon the conventional enthalpic LBM framework by seamlessly incorporating tailored source terms, enabling precise representation of local and transient variations in the medium’s thermophysical properties. The resulting LBM model comprehensively captures the energy conservation equation, with exceptions made only for flow compressibility and viscous dissipation, thereby significantly augmenting its versatility in analyzing heat exchanger configurations. Verification tests, comprising assessments of both transient and steady-state solutions, unequivocally validate the accuracy of the proposed model, further bolstering its reliability for analyzing heat exchange processes within intricate heat exchanger geometries. To demonstrate its efficacy, simulations of conjugate heat transfer processes involving fluid natural convection within structured cavities were performed, imposing both Dirichlet and Neumann boundary conditions to emulate scenarios encountered in practical heat exchanger operations. The findings yield compelling insights, particularly in the transient regime, revealing the beneficial impact of structured cavities on enhancing heat transfer processes. These insights inform potential design optimizations for heat exchangers. The results emphasize the potential of the modified enthalpic LBM approach to elucidate complex heat transfer phenomena in non-homogeneous media and structured geometries, offering valuable implications for heat exchanger engineering and optimization.