Various boron only ([B]-BEA) as well as aluminum- and boron-containing beta zeolites ([Al,B]-BEA) have been prepared and modified by ion exchange of ammonium, sodium, and nickel ions. The zeolite samples have been characterized by 11B, 27Al, and 29Si MAS as well as three of them by 11B and 27Al 3Q-MAS NMR spectroscopy. The quantitative contributions of defect-free Si(nX) (n = 2, 1, 0; X = Al, B) and Si(OH)x (x = 2, 1) sites to the NMR signal intensities were calculated from the various Si/(Al + B) ratios and relative 11B, 27Al, and 29Si NMR signal intensities using the special distribution of aluminum and boron in different periodical building units of the zeolite framework. The boron atoms are sitting exclusively in diagonal positions in the four-membered rings of [B]-BEA zeolites, while the aluminum atoms are situated both in diagonal and lone positions in the four-membered rings of [Al,B]-BEA zeolites. A higher part of boron atoms are positioned in framework-related deformed tetrahedral boron species than in lattice positions in the [B]-BEA than in the [Al,B]-BEA zeolites. All extraframework octahedral aluminum species are transformed back to lattice positions due to ion exchange from the protonated form to ammonium-, sodium-, or nickel-ions containing zeolites. Oppositely, trigonal boron leaves the zeolite structure completely during ion exchange.