Berry fruits, such as strawberries and blueberries, are rich sources of anthocyanins. Several studies have been made on the impact of non-thermal treatments on safety, shelf-life and nutritional characteristics of such products, but the effects of these processes on anthocyanin stability during digestion in the gastrointestinal tract are still not completely clear. The aim of this study was to assess the recovery of anthocyanins after simulated gastrointestinal digestion of (1) strawberry samples, pre-treated with pulsed electric field (PEF) at 100 or 200 V·cm−1, prior to osmotic dehydration (OD), and (2) blueberry samples coated with chitosan and procyanidin. After digestion, a significantly higher content of cyanidin-3-O-glucoside and malvidin-3-O-glucoside was quantified by LC-MS/MS in processed strawberry and blueberry samples, compared with the controls. The highest recovery of cyanidin-3-O-glucoside was detected in digested strawberry samples osmotically dehydrated with trehalose. The recovery of malvidin-3-O-glucoside was highest in digested blueberries coated with chitosan and stored for 14 days, compared with untreated samples or samples coated with chitosan and procyanidin. Our study shows the potential of mild PEF treatments combined with OD, or the use of edible coating, to obtain shelf-stable products without substantially affecting the composition or the stability of anthocyanins during digestion in the upper gastrointestinal tract.