The TNU-9 zeolite (TUN framework) is one of the most complex zeolites known. It represents a highly promising matrix for both acid and redox catalytic reactions. We present here a newly developed approach involving the use of Si and Al (3Q) MAS NMR spectroscopy, Co as probes monitored by UV/Vis and FTIR spectroscopy, and extensive periodic DFT calculations, including molecular dynamics, to investigating the aluminum distribution in the TUN framework and the location of aluminum pairs and divalent cations in extra-framework cationic positions. Our study reveals that 40 and 60 % of aluminum atoms in the TNU-9 zeolite are isolated single aluminum atoms and aluminum pairs, respectively. The aluminum pairs are present in two types of six-membered rings forming the corresponding α and β (15 and 85 %, respectively, of aluminum pairs) sites of bare divalent cations. The α site is located on the TUN straight channel wall and it connects two channel intersections. The suggested near-planar β site is present at the channel intersection.