Herein, we report on adenine, D-ribose, and monophosphate adsorption/co-adsorption into the synthetic analog of the zeolite mineral mordenite followed by drying at 50 °C and thermal activation at 150 °C under an argon atmosphere. Adenine/mordenite samples were prepared first and then used to co-adsorb D-ribose (1 : 1 molar) and monophosphate (1 : 2 molar). The optimal conditions to charge adenine into mordenite were pH 3, contact time of 5 min and 1300 mg L−1 of Ci, resulting in the maximum adsorption of 65.6 μg g−1. The drying and thermal activation effects in the adsorbed/co-adsorbed confined species were followed by FTIR, TGA, 31P and 13C CP-MAS and solid-state NMR. From the results, the electrostatic interaction was proposed as the main mechanism for adenine adsorption into mordenite. The stabilization of α- and β-D-ribofuranose enantiomers and condensation reactions involving D-ribose and inorganic monophosphate were also evidenced even at 50 °C. Data suggested the mordenite micropore space may play a role in the origins of life both to adsorb and concentrate prebiotic molecules and to promote isomerization and condensation reactions to nucleotides from their building blocks.