Dipicolinic acid (DPA) was crystallised in microemulsions to investigate the effect of 3D nanoconfinement on the crystallisation process. The microemulsions were acidified with 2M HCl to prevent the formation of DPA metal salts, which occurs due to a pH shift towards neutrality arising from the nanoconfinement. TEM analysis showed that 30-100 nm square-plate nanoaggregates crystallised from these acidified microemulsions. Higher resolution TEM images revealed that the nanoaggregates consisted of smaller 3-10 nm nanocrystals. The FFT’s obtained from images of these nanocrystals were similar to the diffraction pattern arising from the whole nanoaggregate confirming that the nanocrystals exhibited ordered packing and resembled mesocrystals. The crystallisation of the nanoaggregates is aided by the suppression of Ostwald ripening of the nanocrystals in the nm-sized microemulsion droplets and surfactant adsorption onto the nanocrystals.