Ni, Co, and Zn are widely distributed in the Earth’s mantle as significant minor elements that may offer insights into the chemistry of melting in the mantle. To better understand the distribution of Ni2+, Co2+, and Zn2+ in the most abundant silicate phases in the transition zone and the upper mantle, we have analyzed the crystal chemistry of wadsleyite (Mg2SiO4), ringwoodite (Mg2SiO4), forsterite (Mg2SiO4), and clinoenstatite (Mg2Si2O6) synthesized at 12–20 GPa and 1200–1400 °C with 1.5–3 wt% of either NiO, CoO, or ZnO in starting materials. Single-crystal X-ray diffraction analyses demonstrate that significant amounts of Ni, Co, and Zn are incorporated in octahedral sites in wadsleyite (up to 7.1 at%), ringwoodite (up to 11.3 at%), olivine (up to 2.0 at%), and clinoenstatite (up to 3.2 at%). Crystal structure refinements indicate that crystal field stabilization energy (CFSE) controls both cation ordering and transition metal partitioning in coexisting minerals. According to electron microprobe analyses, Ni and Co partition preferentially into forsterite and wadsleyite relative to coexisting clinoenstatite. Ni strongly prefers ringwoodite over coexisting wadsleyite with $${D}_{\text{Ni}}^{\text{Rw}/\text{Wd}}$$ DNiRw/Wd = 4.13. Due to decreasing metal–oxygen distances with rising pressure, crystal field effect on distribution of divalent metal ions in magnesium silicates is more critical in the transition zone relative to the upper mantle. Analyses of Ni partitioning between the major upper-mantle phases implies that Ni-rich olivine in ultramafic rocks can be indicative of near-primary magmas.