Croplands in the Comarca Lagunera region of Mexico are undergoing abandonment due to water scarcity. The effects of vegetation succession following cropland abandonment on soil organic carbon (SOC) and total nitrogen (STN) stocks have been poorly studied although such effects have important implications for terrestrial carbon pools and the global carbon cycle. This study sought to determine the organic carbon and total nitrogen content in soil at two depths (0–30 cm and 30–60 cm) and the successional biomass with a chronosequence of 2, 15, 25, and 35 years of restoration after cropland abandonment, as well as uncultivated areas of native microphyllous desert scrub vegetation used as reference (Ref). Results revealed that the ecological succession 35 years after cropland abandonment resulted in high dominance by the species Prosopis glandulosa. Because of that, the latest stage since cropland abandonment (35 years) contained about three times more carbon and nitrogen (2.64 Mg C ha−1 and 0.62 Mg N ha−1, respectively) in aboveground biomass than reference areas (0.94 Mg C ha−1 and 0.21 Mg N ha−1, respectively). In contrast, soil carbon tended to decrease as years of abandonment increased. Thus, areas with 35 years of abandonment, although having high aerial carbon content, had the lowest soil carbon accumulation. Soil organic carbon and total nitrogen content showed no significant differences between the sampling depths in the investigated sites during the restoration time. These findings suggest that soil carbon accumulation after cropland abandonment through unmanaged ecological succession is difficult to achieve in this area.