Atmospheric changes, including high CO2 concentration, air temperature and tropospheric ozone concentration, are challenging our crop cultivation systems, with potential negative implications for global food production. Atmospheric changes directly affect different physiological processes, and furthermore modify the whole agro-ecosystem functioning through complex interactions with other environmental factors, including nutrient or water availability. Research in various experimental set-ups currently contributes to unravel the crop responses. Elevated CO2 concentration is now known for its fertilizing and positive impact on crop yield and water use, whereas heat stress and increased ozone concentrations reduce crop yields. Besides yield quantity, also yield quality is affected with CO2-induced reduction but ozone-induced enhancement of crops’ nitrogen and protein concentrations. More scientific research has a significant role to play in the development of sustainable adaptation and innovation answers to the observed atmospheric changes.