The developing Human Connectome Project (dHCP) is a collaborative 6-year project set to create a 4-dimensional map of structural and functional changes occurring throughout early development. Up to 1300 multi-modal MRI scans of foetuses and neonates (20 to 44 weeks gestational age) are currently being acquired. We present a fully automated pre-processing pipeline that allows us to efficiently analyse in-vivo diffusion MRI (dMRI) data despite the considerable technical challenges specific to neonatal imaging. We developed a quality control (QC) framework that allows us to identify issues or inconsistencies. This is especially useful when processing a very large number of subjects.