We have studied the effect of irreversibility induced by repeated thermal cycles on the electric transport and magnetization of polycrystalline samples of La_0.5Ca_0.5MnO₃ and La_0.325Pr_0.3Ca_0.375MnO₃. An increase of the resistivity and a decrease of the magnetization at different temperature ranges after cycling is obtained in the temperature range between 300 K and 30 K. Both compounds are known to exhibit intrinsic submicrometric coexistence of phases and undergo a sequence of phase transitions related to structural changes. Changes induced by thermal cycling can be partially inhibited by applying magnetic field and hydrostatic pressure. Our results suggest that the growth and coexistence of phases with different structures gives rise to microstructural tracks and strain accommodation, producing the observed irreversibility. Irrespective of the actual ground state of each compound, the effect of thermal cycling is towards an increase of the amount of the insulating phase in both compounds.