Atmospheric CO2 elevation (e[CO2]) could alleviate the impact of soil water deficit, yet the underlying mechanisms remains largely elusive. This study aimed to investigate whether different endogenous abscisic acid (ABA) level modulates the response of barley and tomato plants to soil water deficit combined with e[CO2]. Wild type (WT) genotypes (Steptoe barley and AC tomato) and their corresponding ABA-deficient mutants (Az34 barley and AC-flacca) were grown in pots separately in greenhouse cells with ambient (a[CO2], 400 ppm) and e[CO2] (800 ppm) and were either well-watered or exposed to soil water deficit. The results showed that, compared to well-watered regime, soil water deficit decreased aboveground dry matter (ADM), leaf area (LA) and specific leaf area (SLA) while enhanced water use efficiency (WUE) in all genotypes. e[CO2] increased ADM and LA in tomato genotypes. Moreover, it reduced SLA, leaf N concentration while improved WUE and nitrogen use efficiency (NUE) in WT plants, not in ABA-deficient mutants. These results indicate that endogenous ABA level played an important role in modulating the response of WUE and NUE of barley and tomato to e[CO2] environment, which advances our knowledge on the physiological mechanisms of crop plants adapt to future climate changed scenarios.