The spatial organization of porous coordination polymer (PCP) crystals into higher-order structures is critical for their integration into separation systems, heterogeneous catalysts, ion/electron transport and photonic devices. Here, we demonstrate a rapid method to spatially control the nucleation site, leading to the formation of mesoscopic architecture made of PCPs, in both two and three dimensions. Inspired by geological processes, this method relies on the morphological replacement of a shaped sacrificial metal oxide used both as a metal source and as an ‘architecture-directing agent’ by an analogous PCP architecture. Spatiotemporal harmonization of the metal oxide dissolution and the PCP crystallization allowed the preservation of very fine mineral morphological details of periodic alumina inverse opal structures. The replication of randomly structured alumina aerogels resulted in a PCP architecture with hierarchical porosity in which the hydrophobic micropores of the PCP and the mesopores/macropores inherited from the parent aerogels synergistically enhanced the material’s selectivity and mass transfer for water/ethanol separation.