SUMMARYAdvances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic ‘big' omics data’ of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross‐species, meta‐) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature‐inspired to fully synthetic parts has already allowed building of fine‐tuned regulatory circuits, or new‐to‐nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species‐agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.