This article contains data of time of flight secondary ion mass spectrometry (TOF-SIMS) analysis of brushite-forming calcium phosphate cements doped with biologically active metal ions. This data are related to the research article “Cu²⁺, Co²⁺ and Cr³⁺ doping of a calcium phosphate cement influences materials properties and response of human mesenchymal stromal cells” (Schamel et al., 2017) [1]. Cu²⁺, Co²⁺ and Cr³⁺ doped β-tricalcium phosphate precursor powders were used to prepare cement samples. The incorporation and distribution of the metal ions in the cement matrix was visualized by imaging mass spectrometry.