Crystallisation of the earliest minerals typically affects the composition of minerals subsequently formed, being controlled by their abundance and the compatibility/incompatibility of the relevant elements. Here we have investigated the effects of early tourmaline crystallisation on the formation of primary Be minerals (beryl and helvine–danalite) in metaluminous intragranitic NYF pegmatites of the Třebíč Pluton, Czech Republic. Tourmaline occurs in different textural-paragenetic types: (a) coarse- to medium-grained aggregates; (b) graphic (Tur+Qz) intergrowths; (c) fine-grained nodules (Tur+Qz+Pl+Kfs); (d) tourmaline pseudomorphs after biotite; (e) interstitial tourmaline; and (f) replacing helvine–danalite. The compositions of primary tourmalines (a), (b) and (c) vary from Ca- and Ti-rich Fe-dravite to Mg-poor schorl and dutrowite, and to magnesio-dutrowite, showing low to moderate Al (5.1–6.1 apfu), variable Mg (0.1–1.9 apfu) and Fe (1.3–2.2 apfu), low Mn (≤0.1 apfu), low to moderate Ca (0.1–0.4 apfu), and high Ti (≤0.55 apfu). Type (f) secondary tourmaline is poor in Mg, Ca and Ti (all ≤0.07 apfu), but rich in Na (0.64–0.81 apfu), Fe (0.68–2.17 apfu), Mn (0.31–0.80 apfu), Al (6.57–7.61 apfu), and F (0.37–0.58 apfu). Two distinct assemblages of early-formed Be minerals were recognised: the assemblage beryl ± phenakite occurs in pegmatites with rare interstitial tourmaline (e), whereas the assemblage helvine–danalite ± phenakite is characteristic of pegmatites with abundant early tourmaline (a). The assemblages of primary Be minerals in the individual pegmatites reflect how crystallisation and abundance of early tourmaline control the origin and composition of successive primary Be minerals. The crystallisation of abundant early-formed tourmaline depletes the residual melt of elements that are incorporated preferentially into the tourmaline structure (Al, Mg, Zn), whereas incompatible Mn accumulates, leading to the formation of Mn-rich helvine–danalite. In contrast, beryl only occurs in pegmatites where early-formed tourmaline is absent. The early crystallisation of tourmaline might thus affect the species and composition of later crystallising minerals.