Recent research on the agricultural impacts of climate change has primarily focused on the roles of temperature and precipitation. These studies show that India has already been negatively affected by recent climate trends. However, anthropogenic climate changes are a result of both global emissions of long-lived greenhouse gases (LLGHGs) and other short-lived climate pollutants (SLCPs). Two potent SLCPs, tropospheric ozone and black carbon, have direct effects on crop yields beyond their indirect effects through climate; emissions of black carbon and ozone precursors have risen dramatically in India over the past three decades. Here, to our knowledge for the first time, we present results of the combined effects of climate change and the direct effects of SLCPs on wheat and rice yields in India from 1980 to 2010. Our statistical model suggests that, averaged over India, yields in 2010 were up to 36% lower for wheat than they otherwise would have been, absent climate and pollutant emissions trends, with some densely populated states experiencing 50% relative yield losses. [Our point estimates for rice (-20%) are similarly large, but not statistically significant.] Upper-bound estimates suggest that an overwhelming fraction (90%) of these losses is due to the direct effects of SLCPs. Gains from addressing regional air pollution could thus counter expected future yield losses resulting from direct climate change effects of LLGHGs.