In this work we find a novel conformational sieving effect during the structuredirection of two chiral organic diastereoisomers, (1R,2S)-benzyl-ephedrine and (1S,2S)benzyl-pseudoephedrine, during the synthesis of zeolitic aluminophosphates. Protonation of each diastereoisomer can take place through two different stereochemical configurations, giving place to a new stereogenic N center that results in two stereoisomers for each molecule, with (1R,2S,NS) or (1R,2S,NR) configurations for benzyl-ephedrine or (1S,2S,NR) or (1S,2S,NS) configurations for benzylpseudoephedrine. Through a combination of 1 H and 13 C NMR spectroscopies and DFT+D computational calculations we are able to distinguish the two stereoisomers derived from benzyl-pseudoephedrine: results show a higher occurrence of the (1S,2S,NS) isomer in aqueous solution, displaying a folded molecular configuration, while the less abundant (1S,2S,NR) isomer displays instead a conformation with an elongated shape.Crystallization of microporous aluminophosphates in the presence of benzylpseudoephedrine results in materials with AFI structure based on one-dimensional channels with a surprising higher occurrence of the (1S,2S,NR) isomer, in sharp contrast with the behavior in aqueous solution. Such notable difference is ascribed to the elongated shape of the (1S,2S,NR) stereoisomer that can better fit within the AFI one-dimensional nano-channels. On the other hand, assignment of the 1 H and 13 C NMR bands to the different protonated stereoisomers of (1R,2S)-benzyl-ephedrine is not as clear due to the smaller splitting of the signals upon protonation through the two stereochemical configurations. This work demonstrates that confinement in nano-spaces can alter the relative stability of stereoisomers in open spaces, leading to the occurrence of species that would not be possible otherwise.