Microwave resonator measurements were performed on high‐performance microwave ceramics Ba(Zn1/3Ta2/3)O3 (BZT) and Ba(Zn1/3Nb2/3)O3 (BZN) containing additives commonly used by commercial manufacturers (i.e., Co, Mn, and Ni). We find that the loss tangent, even in ambient magnetic fields, is dominated by electron paramagnetic resonance (EPR) absorption by exchange‐coupled 3d electrons in transition metal clusters at cryogenic temperatures. The large orbital angular momentum in Co2+ and Ni2+ ions of L = 3 causes strong anisotropic‐broadened dipolar interactions that extend EPR losses to zero applied field. This effect is greatest in BZN with Co concentrations greater than 0.5 mol%, dominating the losses at liquid nitrogen temperatures (77 K) and below. In samples containing Mn2+ ions with L = 0, the dipolar interactions and associated EPR losses in ambient fields are smaller. We show the magnetic‐field‐dependent changes in the EPR losses (i.e., tan δ) and magnetic reactive response (i.e., μr) are from the same mechanism, as they follow the Kramers–Kronig relation. Finally, we note that these materials can make ultra‐high Q passive microwave devices with externally controlled transfer functions, as the quality factor (Q) of the composition Ba(Co1/15Zn4/15Nb2/3)O3 at 77 K can be tuned from 1 100 to 12 000 at 10 GHz by applying practical magnetic fields.