Sour cherry pomace filling (SCPF) and commercial sour cherry filling (CSCF) produced on a semi-industrial scale were tested and compared in terms of food safety, chemical composition, bioactivity, quality, sensory properties and thermal stability. Both samples were safe for human consumption, thermally stable and there was a lack of syneresis. SCPF had a significantly higher fiber concentration (3.79 g/100 g) due to higher skin fraction and is considered a “source of fibers”. The higher skin fraction in SCPF also resulted in a higher mineral quantity (Fe—3.83 mg/kg fw) in comparison to CSCF (Fe—2.87 mg/kg fw). Anthocyanins concentration was lower in SCPF (7.58 mg CGE/100 g fw), suggesting that a significant amount of anthocyanins was removed from SC skin during juice extraction. However, there was a lack of statistical differences in antioxidant activity between the two fillings. CSCF was more spreadable, not as firm and less sticky, with lower storage and loss modulus values than SCPF. However, both fillings exhibited acceptable rheological and textural behaviour for fruit fillings. According to the consumer pastry test, 28 participants preferred each pastry; thus, there was a lack of preference toward any of the tested samples. SCP could be used as a raw material for the bakery fruit fillings industry, which leads to the valorization of food industry by-products.