Starch structure and bioactive ingredients play an implicit role in the control of glucose release at intestinal level reducing the risk of inadequate metabolic response(s). This study performs a comparative kinetic approach to glucose release from hydrothermally treated (HT) maize (MS) and quinoa (QS) starch. Besides, chia flour (CF) (20%, w/w) was added to evaluate its influence of on the apparent diffusion coefficients (Dapp) when subjected to simulated gastrointestinal digestion. Hepatocyte cultures were used to monitor mitochondrial enzymes activity (test MTT) to bioaccessible glucose concentrations. With an increasing temperature, Dapp for both QS and its mixtures with CF were kept unaltered, while those for MS were disrupted progressively affecting glucose bioaccessibility. Principal component analysis revealed differences between maize and quinoa starches, but common features in the corresponding mixtures with CF. Data indicated that quinoa starch helps controlling glucose release and that addition of CF decreased mitochondrial activity in presence of insulin.