Secondary‐ion mass spectrometry (SIMS) is used to determine impurity concentrations of carbon and oxygen in two scandium‐containing nitride semiconductor multilayer heterostructures: ScxGa1−xN/GaN and ScxAl1−xN/AlN grown by molecular beam epitaxy (MBE). In the ScxGa1−xN/GaN heterostructure grown in metal‐rich conditions on GaN–SiC template substrates with Sc contents up to 28 at%, the oxygen concentration is found to be below 1 × 1019 cm−3, with an increase directly correlated with the scandium content. In the ScxAl1−xN–AlN heterostructure grown in nitrogen‐rich conditions on AlN–Al2O3 template substrates with Sc contents up to 26 at%, the oxygen concentration is found to be between 1019 and 1021 cm−3, again directly correlated with the Sc content. The increase in oxygen and carbon takes place during the deposition of scandium‐alloyed layers.