Fluorescence spectroscopy and a range of computer simulation techniques are used to study the structure directing effect of benzylpyrrolidine (BP) and (S)-(-)-N-benzylpyrrolidine-2-methanol (BPM) in the synthesis of nanoporous aluminophosphate frameworks with AFI (one-dimensional channels) and SAO (three-dimensional interconnected channels) topologies. We study the supramolecular chemistry of BP and BPM molecules in aqueous solution and compare it with the aggregation state of the molecules found when they are inside the AlPO nanopores after crystallization. The aggregation of the molecules within the structures can be explained by a combination of thermodynamic and kinetic effects. The former are given by the stability of the molecular species interacting with the oxide networks relative to their stability in solution; the latter depend on the aggregation behavior of the molecules in the synthesis gels prior to crystallization. Whereas BPM only forms one type of aggregate in solution, which has the appropriate conformation to match the empty channels of the forming nanoporous frameworks, BP forms aggregates with different molecular orientations, of which only one matches the framework interstices. This different supramolecular chemistry, together with the higher interaction of BPM with the oxide networks, makes BPM a better structure directing agent (SDA); it is also responsible for the higher incorporation of BPM as dimers in the frameworks, especially in the AFI structure, observed experimentally. The concentration of the SDA molecules in the gels, and so the density per volume of the SDAs, determines the exclusion zone from which the pores and/or cavities of the framework will arise, and so the porous network of the formed material. A clear relationship between the SDA density in solution and in the framework is observed, thus enabling an eventual control of the material density by adjusting the SDA concentration in the gels. The topological instability intrinsic to these open framework structures is compensated by a high host-guest interaction energy; the SAO topology is further stabilized by doping with Zn. Our computational results account for and rationalize all the effects observed experimentally, providing a complete picture of the mode of structure direction of these aromatic molecules in the synthesis of nanoporous aluminophosphates.