Oxygen deficient double perovskite Sr2MnNbO6−𝛿 was studied by means of X-ray and neutron diffraction, X-ray fluorescence, magnitometry, specific heat, and electron spin resonance (ESR) methods. By the method of neutron diffraction, it was found that the compound crystallizes in a space group 𝑃𝑏𝑛𝑚 in temperature range 4–300 K. X-ray fluorescence data indicate a deviation from stoichiometric composition, which leads to a variable valence of manganese ions with the existence of ions with different spins, Mn4+ (𝑆 = 3∕2), Mn3+ (𝑆 = 2), and Mn2+ (𝑆 = 5∕2) ions. The Curie temperature 𝑇C = 42.4 K was obtained from magnetization, specific heat, and ESR measurements. Some anomalies were observed at 𝑇 = 6.7 K, 12.7 K, and 38.9 K in the temperature dependencies of AC magnetization and specific heat measurements. Hysteresis loops were observed in the sample in the 𝑇 = 5–42 K range. Our analysis revealed two ESR lines with small and large linewidths in the vicinity of 𝑔 ≈ 2 associated with magnetic phase separation. We provide a discussion of dynamic relaxation processes in this compound based on the temperature dependencies of the ESR linewidth. The third ESR line with 𝐻𝑟𝑒𝑠 ≈ 500 Oe in X- and Q-bands was observed in temperature range 38–44 K (temperature range is 2 K wider, than in magnetization measurements), confirming the peaks of the AC magnetization. We believe that the third ESR signal is related to the spin-flop transition.