We develop a new methodology for spatial regression of aggregated outputs on multi-resolution covariates. Such problems often occur with spatial data, for example in crop yield prediction, where the output is spatially-aggregated over an area and the covariates may be observed at multiple resolutions. Building upon previous work on aggregated output regression, we propose a regression framework to synthesise the effects of the covariates at different resolutions on the output and provide uncertainty estimation. We show that, for a crop yield prediction problem, our approach is more scalable, via variational inference, than existing multi-resolution regression models. We also show that our framework yields good predictive performance, compared to existing multi-resolution crop yield models, whilst being able to provide estimation of the underlying spatial effects.