The adsorption, partitioning, and diffusion of CO2 and CH4 in organic-inorganic pores composed of kerogen with silica, illite, or calcite are studied using density functional theory and classical molecular dynamics simulations. The adsorption and partitioning behavior of CO2 and CH4 molecules is found to be a function of chemistry of the solid interface, pore size, and surface area. CO2 molecules are preferentially adsorbed compared to CH4 molecules on silica, illite, calcite, and kerogen surfaces due to significant contributions of electrostatic interactions with the atoms of the associated surfaces. CO2 and CH4 molecules display higher adsorption energy on calcite and silica compared to those on illite and kerogen because of enhanced interactions with the positively charged calcium ions on the calcite surface and the hydroxyl group (-OH) on the silica surface. Enhanced internal nanopores and the availability of adsorption active sites in illite and kerogen matrices aid in higher partitioning of the gas molecules into these pores. CO2 has a significant influence on the clustering and swelling of kerogen fragments compared to CH4. Higher CO2 adsorption on inorganic and kerogen surfaces results in lower overall self-diffusivities compared to CH4. This study illustrates surface and pore size controls on the adsorption, partitioning, and self-diffusivities of CO2 and CH4 at conditions relevant for subsurface energy applications. The chemistry of the surfaces along with the availability of internal pores and active adsorption sites influences the adsorption behavior of gases. Our results suggest that CO2 stored in depleted gas reservoirs may preferentially inhabit nanoconfined pores.