Small pore size and hydrophobic nature of DD3R make this material a unique zeolite with high potential in industrial separation applications. However, the reproducible rapid synthesis of this zeolite is still a problem. In this work, a thorough assessment of different synthetic methods revealed that synthesis reproducibility relies on two main pillars: the use of properly cleaned autoclave liners and the synthesis composition. High quality DD3R crystals are obtained when KOH is used as a cleaning agent, eliminating memory effects, and when KF is used in the synthesis as a mineralizing agent. The effect of fluoride addition is investigated by use of several characterization techniques (13C, 19F and 29Si MAS-NMR and (2D) 29Si–1H correlation spectra), while monitoring the temporal crystallization of DDR. 29Si–1H NMR reveals that template molecules accommodated within the cages are sticking to these 8-ring windows through their amine group. High quality DD3R crystals are applied in the adsorptive separation of buta-1,3-diene and but-2-ene isomers, one of the most energy intensive separations in chemical industry. Mixture separation experiments revealed that the 8-ring apertures of the DD3R cages are only accessible to trans-but-2-ene and buta-1,3-diene, while excluding but-1-ene and cis-but-2-ene molecules, resulting in shape-selective separation in the presence of C4 mixtures.