Background: Cocoa ( Theobroma cacao L.) is a crop of huge economic significance worldwide and is grown mainly in tropical and subtropical countries. Currently, West Africa produces most of the world's cocoa. The crop provides economic support to cocoa-growing countries, smallholder farmers, and the chocolate confectionery industries. Cocoa is also valued for its appealing flavours and the health-promoting properties of the bioactive phytochemicals in the beans, which have received increased global attention in recent years. Main body: The cocoa industry is divided into two sectors: upstream (cocoa bean production and marketing), which is dominated by cocoa-producing countries, and downstream (cocoa bean processing activities to produce semi-finished and finished products). Pests and diseases, climate change, low soil fertility, high soil cadmium levels, and the ongoing Russian-Ukrainian conflict threaten the crop's long-term production. In addition to these challenges, cocoa cultivation also contributes to environmental and biodiversity degradation. Conclusion: To address these challenges and ensure a sustainable supply of high-quality cocoa beans to meet the rising global demand, sustainable intensification of its production in producing countries is deemed critical. These include breeding varieties that are resistant to yield-limiting factors, the use of integrated management strategies to improve soil fertility and control pests, diseases, and heavy metals like Cd, the implementation of agroforestry systems, increased farm gate prices, and the provision of social interventions such as alternative livelihoods for farmers to increase cocoa production on existing farmlands. Standardized and harmonized farm management and postharvest strategies are also required for the consistent production of high-quality beans each season.

Despite the health benefits associated with the ingestion of the bioactive compounds in cocoa, the high concentrations of polyphenols and methylxanthines in the raw cocoa beans negatively influence the taste, confer the astringency and bitterness, and affect the stability and digestibility of the cocoa products. It is, therefore, necessary to process cocoa beans to develop the characteristic color, taste, and flavor, and reduce the astringency and bitterness, which are desirable in cocoa products. Processing, however, affects the composition and quantities of the bioactive compounds, resulting in the modification of the health-promoting properties of cocoa beans and chocolate. In this advanced review, we sought to better understand the effect of cocoa’s transformational process into chocolate on polyphenols and methylxanthine and the mechanism of action of the original flavanols and methylxanthines. More data on the cocoa processing effect on cocoa bioactives are still needed for better understanding the effect of each processing step on the final polyphenolic and methylxanthine composition of chocolate and other cocoa products. Regarding the mechanisms of action, theobromine acts through the modulation of the fatty acid metabolism, mitochondrial function, and energy metabolism pathways, while flavanols mainly act though the protein kinases and antioxidant pathways. Both flavanols and theobromine seem to be involved in the nitric oxide and neurotrophin regulation.