Agro-industrial by-products are promising source of biopolymers, including proteins and polysaccharides. This study was designed to evaluate the flaxseed oil cake extract (FOCE) as natural encapsulating material and carrier for probiotic Lacticaseibacillus rhamnous GG (LGG). The powders were obtained using three spray drying inlet temperatures (110 °C, 140 °C, 170 °C), and reconstituted. The influence of temperature on water activity, morphology, chemical composition, flowability and cohesiveness of the powders was estimated. For all variants, the survival of bacteria during spray drying, and simulated passage through the gastrointestinal tract was evaluated. The preservation of LGG probiotic features such as cholesterol reduction, hydrophobicity and adhesion to mucin were examined. Results revealed that all physicochemical and functional characteristics of the powders were affected by the inlet temperature. This study demonstrated that FOCE is an appropriate matrix for spray drying (due to flaxseed proteins and polysaccharides) providing high survivability of bacteria (89.41–96.32%), that passed meaningfully through the simulated gastrointestinal tract (4.39–5.97 log reduction), largely maintaining their probiotic properties, being a promising environmentally-friendly carrier for probiotic LGG.