This work provides insights into the deterioration of cacti seeds of Escontria chiotilla (F.A.C. Weber ex K. Schum) and Stenocereus pruinosus (Otto ex Pfeiff.) Buxbaum stored ex situ at 25 °C, under dry and dark conditions or buried in situ conditions in a xerophytic shrubland. Viability, germination speed, electrolyte leakage and indicators of the redox balance including glutathione content, glutathione half-cell reduction potential (EGSSG/2GSH) and malondialdehyde (MDA), oxidized protein content, together with water-soluble antioxidant enzyme activity were assessed. Over a period of two years of storage, viability was maintained when seeds were stored ex situ at 7–9% water content compared to seeds buried in the soil. A second burial experiment showed that seeds of E. chiotilla maintained viability during a year of storage that included a rainy season followed by a dry season. Thereafter, they died rapidly during the second rainy season. In contrast, those of S. pruinosus started to lose viability after 6 months of burial at the end of the rainy season and were mostly dead at the end of the dry season. This difference in persistence between species was related to a difference in the glutathione content and antioxidant enzyme activities. In both storage experiments, the loss of viability of both species was associated to a EGSSG/2GSH shift to a more oxidative state during burial. Yet, contents in MDA and oxidized soluble proteins were not related to redox imbalance and loss of viability, indicating that these compounds are not good markers of oxidative stress in cacti seeds during storage.