To reduce the emissions of internal combustion engines, ceria-based catalysts have been widely investigated as possible alternatives to the more expensive noble metals. In the present work, a set of four different ceria-based materials was prepared via hydrothermal synthesis, studying the effect of Cu and Mn as dopants both in binary and ternary oxides. In situ Raman analyses were carried out to monitor the behaviour of defect sites throughout thermal cycles and during the soot oxidation reaction. Despite ceria doped with 5% of Cu featured the highest specific surface area, reducibility and amount of intrinsic and extrinsic defects, a poor soot oxidation activity was observed through the standard activity tests. This result was confirmed by the calculation of soot conversion curves obtained through a newly proposed procedure, starting from the Raman spectra collected during the in situ tests. Moreover, Raman analyses highlighted that new defectiveness was produced on the Cu-doped catalyst at high temperature, especially after soot conversion, while a slight increase of the defect band and a total reversibility were observed in case of the ternary oxide and pure/Mn-doped ceria, respectively. The major increment was related to the extrinsic defects component; tests carried out in different atmospheres suggested the assignment of this feature to vacancy-free sites containing oxidized doping cations. Its increase at the end of the tests can be an evidence of peroxides and superoxides deactivation on catalysts presenting excessive oxygen vacancy concentrations. Instead, ceria doped with 5% of Mn exhibited the best soot oxidation activity, thanks to an intermediate density of oxygen vacancies and to its well-defined morphology.