Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost one million, and gene expression in half a million, nuclei from eleven tightly staged, overlapping windows of its embryogenesis. Leveraging the asynchronicity of embryos within each collection, we developed a statistical model to more precisely estimate the age of each nucleus, resulting in continuous views of molecular and cellular transitions throughout the majority of embryonic development. From these data, we identify cell types, infer their developmental relationships, and link cell type-specific changes to dynamic changes in enhancer usage, transcription factor (TF) expression and the accessibility of TFs' cognate motifs. Looking forward, this strategy may facilitate future investigations of gene regulation in vivo at arbitrarily high temporal resolution.