Magnetic topological insulators (TIs) herald a wealth of applications in spin‐based technologies, relying on the novel quantum phenomena provided by their topological properties. Particularly promising is the (MnBi2Te4)(Bi2Te3)n layered family of established intrinsic magnetic TIs that can flexibly realize various magnetic orders and topological states. High tunability of this material platform is enabled by manganese–pnictogen intermixing, whose amounts and distribution patterns are controlled by synthetic conditions. Here, nuclear magnetic resonance and muon spin spectroscopy, sensitive local probe techniques, are employed to scrutinize the impact of the intermixing on the magnetic properties of (MnBi2Te4)(Bi2Te3)n and MnSb2Te4. The measurements not only confirm the opposite alignment between the Mn magnetic moments on native sites and antisites in the ground state of MnSb2Te4, but for the first time directly show the same alignment in (MnBi2Te4)(Bi2Te3)n with n = 0, 1 and 2. Moreover, for all compounds, the static magnetic moment of the Mn antisite sublattice is found to disappear well below the intrinsic magnetic transition temperature, leaving a homogeneous magnetic structure undisturbed by the intermixing. The findings provide a microscopic understanding of the crucial role played by Mn–Bi intermixing in (MnBi2Te4)(Bi2Te3)n and offer pathways to optimizing the magnetic gap in its surface states.