The United Kingdom has begun investing in sustainable manufacturing as part of comprehensive policy aimed at addressing climate change. Pharmaceutical production accounts for 5% of the UK’s total carbon footprint; a significant portion of this is linked directly to feedstock used in bacterial fermentation biofactories. As natural producers of many antimicrobial compounds, Streptomyces bacteria have been optimised over the course of decades for drug manufacture via these large scale fermentations. Alternate feedstocks, like bread waste, have the potential to significantly reduce the environmental impact of antimicrobial production. However, current productions strains exhibit reduced antibiotic yield when using alternate carbon sources due to close regulation of carbon metabolism. To understand the mechanisms of this regulation, we use transcriptomic and metabolomic data to create detailed maps of several carbon metabolism and antibiotic pathways in Streptomyces clavuligerus production strains. The dataset allows us to visualise changes at each step in a pathway over time, and between carbon sources. This will inform the design of high titre production strains that can utilise environmentally conscious carbon sources, ultimately reducing the carbon footprint without sacrificing drug yield. This approach can also be adapted in other organisms to address sustainable drug manufacture across the industry.