We consider the impact of key astrophysical and measurement systematics on constraints on dark energy and modifications to gravity on cosmic scales. We focus on upcoming photometric ‘stage III’ and ‘stage IV’ large‐scale structure surveys such as the Dark Energy Survey (DES), the Subaru Measurement of Images and Redshifts survey, the Euclid survey, the Large Synoptic Survey Telescope (LSST) and Wide Field Infra‐Red Space Telescope (WFIRST). We illustrate the different redshift dependencies of gravity modifications compared to intrinsic alignments, the main astrophysical systematic. The way in which systematic uncertainties, such as galaxy bias and intrinsic alignments, are modelled can change dark energy equation‐of‐state parameter and modified gravity figures of merit by a factor of 4. The inclusion of cross‐correlations of cosmic shear and galaxy position measurements helps reduce the loss of constraining power from the lensing shear surveys. When forecasts for Planck cosmic microwave background and stage IV surveys are combined, constraints on the dark energy equation‐of‐state parameter and modified gravity model are recovered, relative to those from shear data with no systematic uncertainties, provided fewer than 36 free parameters in total are used to describe the galaxy bias and intrinsic alignment models as a function of scale and redshift. While some uncertainty in the intrinsic alignment (IA) model can be tolerated, it is going to be important to be able to parametrize IAs well in order to realize the full potential of upcoming surveys. To facilitate future investigations, we also provide a fitting function for the matter power spectrum arising from the phenomenological modified gravity model we consider.