Nanostructured materials derived from sustainable sources are of interest as viable alternatives to traditional petroleum-derived sources in membrane applications due to environmental concerns. Here, we present the development of pore size-tunable nanostructured polymer membranes based on a plant-derived material. The membranes were fabricated using a tri-functional amine as the templating core species and a cross-linkable ligand synthesized from rose oil-derived citronellol. The self-assembly of a supramolecular complex between the template core and the ligand forms a hexagonally packed columnar (Colh) mesophase, the dimensions of which can be precisely controlled by changing the stoichiometric ratio between these constituents. Within the hexagonal mesophase stoichiometric range, the pore size of the nanostructured membranes can be tuned from 1.0 to 1.3 nm, with a step size of approximately 0.1 nm. The membranes exhibited a clear distinction in molecular size selectivity, as demonstrated by dye adsorption experiments. The membrane fabricated with a ligand-to-core ratio of 3 to 1 demonstrated shape-based selectivity, exhibiting a higher permeability for propeller-shaped penetrants and highlighting its potential for shape-selective transport. We anticipate that this straightforward approach, using plant-derived materials, can contribute to important sustainability aspects while enhancing the performance of current state-of-the-art nanostructured membranes by enabling precise control over pore size.