Chocolate production faces nutritional, environmental and socio-economic challenges present in the conventional cocoa value chain. Here we developed an approach that addresses these challenges by repurposing the often-discarded pectin-rich cocoa pod endocarp and converting it into a gel. This is done using cocoa pulp juice concentrate to replace traditional sugar from sugar beets. Although swelling of fibres, proteins and starches can limit gel incorporation, our proposed chocolate formulation contains up to 20 wt% gel. It also has comparable sweet taste as traditional chocolate while offering improved nutritional value with higher fibre and reduced saturated fatty acid content. A cradle-to-factory life cycle assessment shows that large-scale production of this chocolate could reduce land use and global warming potential compared with average European dark chocolate production. The process also provides opportunities for diversification of farmers’ income and technology transfer, offering potential socio-economic benefits for cocoa-producing regions.