Thermal fatigue is a common failure mode in electronic solder joints, yet the role of microstructure is incompletely understood. Here, we quantify the evolution of microstructure and damage in Sn-3Ag-0.5Cu joints throughout a ball grid array (BGA) package using EBSD mapping of localised subgrains, recrystallisation and heavily coarsened Ag3Sn. We then interpret the results with a multi-scale modelling approach that links from a continuum model at the package/board scale through to a crystal plasticity finite element model at the microstructure scale. We measure and explain the dependence of damage evolution on (i) the β-Sn crystal orientation(s) in single and multigrain joints, and (ii) the coefficient of thermal expansion (CTE) mismatch between tin grains in cyclic twinned multigrain joints. We further explore the relative importance of the solder microstructure versus the joint location in the array. The results provide a basis for designing optimum solder joint microstructures for thermal fatigue resistance.