Rising tropospheric ozone is a major threat to the crops in the present climate change scenario. To investigate the EDU induced changes in proteins, two varieties of maize, the SHM3031 and the PEHM5, (hereafter S and P respectively) were treated with three EDU applications (0 = control, 50 and 200 ppm) (hereafter 0 = A, 1 and 2 respectively) (SA, S1, S2, PA, P1, P2 cultivar X treatments). Data on the morpho-physiology, enzymatic activity, and protein expression (for the first time) were collected at the vegetative (V, 45 DAG) and flowering (F, 75 DAG) developmental stages. The tropospheric ozone was around 53 ppb enough to cause phytotoxic effects. Protective effects of EDU were recorded in morpho-physiologically and biochemically. SOD, CAT and APX together with GR performed better under EDU protection in SHM3031 variety than PEHM5. The protein expression patterns in SHM3031 at the vegetative stage (28% proteins were increased, 7% were decreased), and at the flowering stage (17% increased, 8% decreased) were found. In PEHM5, a 14% increase and an 18% decrease (vegetative stage) whereas a 16% increase and a 20% decrease (flowering stage) were recorded in protein expression. Some protein functional categories, for instance, photosynthesis, carbon metabolism, energy metabolism, and defense were influenced by EDU. Rubisco expression was increased in SHM3031 whereas differentially expressed in PEHM5. Germin like protein, APX, SOD, and harpin binding proteins have enhanced defense regulatory mechanisms under EDU treatment during prevailing high tropospheric O-3. The present study showed EDU protective roles in C4 plants as proven in C3.