Mathematical models are the most cost-effective way to learn about a system. The objective of this study was to identify the model that best describes data for extraction kinetics of flavonoids released from cocoa (Theobroma cacao L.) bean shells (CBS) with nine choline chloride-based deep eutectic solvent (ChCl-DES) aqueous solutions. Conventional solvent extraction with an ethanol aqueous solution was used to compare results. Four phenomenological and two empirical models were compared. Flavonoid concentration in the extracts was measured spectrophotometrically and fitted by nonlinear regression. Model goodness-of-fit was evaluated by comparing the adjusted determination coefficient and root mean square error. All the studied models effectively captured the kinetic data by showing a coefficient of determination greater than 0.92. The DES composition influenced the most accurate model. The DES-based extraction notably enhanced the washing and diffusion stages and improved the extraction process.