The emergence of biopolymer building blocks is a crucial step in the origins of life. However, known formation pathways often require rare pure feedstocks and involve complex purification steps to suppress unwanted side reactions. This study demonstrates that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism to separate over 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates, and 2-aminoazoles. Using measured thermophoretic properties, the authors numerically model and experimentally validate the advantageous effect of geological networks of interconnected cracks that purify the compounds, increasing their concentration ratios by up to three orders of magnitude. The importance of this purification is illustrated by the dimerization of glycine, where the selective purification of trimetaphosphate (TMP) increased reaction yields by five orders of magnitude. The observed effect is robust under various conditions, including different crack sizes, pH values, solvents, and temperatures. The results suggest that geologically driven non-equilibria could have explored highly parallelized reaction conditions, fostering prebiotic chemistry.The emergence of biopolymer building blocks is a crucial step in the origins of life. However, known formation pathways often require rare pure feedstocks and involve complex purification steps to suppress unwanted side reactions. This study demonstrates that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism to separate over 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates, and 2-aminoazoles. Using measured thermophoretic properties, the authors numerically model and experimentally validate the advantageous effect of geological networks of interconnected cracks that purify the compounds, increasing their concentration ratios by up to three orders of magnitude. The importance of this purification is illustrated by the dimerization of glycine, where the selective purification of trimetaphosphate (TMP) increased reaction yields by five orders of magnitude. The observed effect is robust under various conditions, including different crack sizes, pH values, solvents, and temperatures. The results suggest that geologically driven non-equilibria could have explored highly parallelized reaction conditions, fostering prebiotic chemistry.