We report the rich magnetic behaviour of Sr2CoNb1-xTixO6 (0 ≤ x ≤ 0.5) oxides as a result of their complex microstructure. Although these oxides show an average simple-cubic perovskite structure, they present a flexible microstructure due to short-range ordering between Co/Ti and Nb cations in the perovskite B-sites. The microstructure consists of double-cubic perovskite domains grown in a simple-cubic perovskite matrix. The size and number of the double-cubic perovskite domains decrease as the Ti content increases. As a result of aliovalent substitution of Nb(5+) by Ti(4+) in the parent Sr2CoNbO6 mixed-valence Co(3+)/Co(4+) oxides are obtained. A spin glass-like state has been observed at low temperatures for all the series, with freezing temperatures increasing with the Ti-content in the range 22 to 33 K. Furthermore, the x = 0.3 and x = 0.5 samples show non-interacting superparamagnetic particle-like dynamics associated with relatively high amounts of Co(4+), with "blocking temperatures" of 13 and ∼16 K, respectively. The complex magnetic behaviour of the title oxides seems to be connected with the clustering of magnetic Co(3+) and the distribution of Co(4+) as a result of the microstructure.