This study investigated the composition of sugars, organic acids, individual and total phenolic compounds in the pulp, peel, leaves, and bark of a red-fleshed ‘Baya Marisa’ apple cultivar. As the fruit is known for its red pulp color, the study focused on comparing the profiles of primary and selected secondary metabolites in three sections along the equatorial fruit plane. The analyses were carried out using HPLC–MS system, and compositional differences were compared among fruit segments. Inner fruit segments accumulated higher levels of sorbitol and the sum of sugars and lower levels of citric acid. However, no differences in the sum of organic acids could be determined among segments. The phenolic composition differed among pulp (hydroxycinnamic acids > dihydrochalcones ≈ anthocyanins ≈ flavanols > flavonols), peel (flavanols > anthocyanins > dihydrochalcones > flavonols > hydroxycinnamic acids), leaves (flavonols > dihydrochalcones > hydroxycinnamic acids > anthocyanins), and bark (dihydrochalcones > flavonols > flavanols > anthocyanins > hydroxycinnamic acids). The greatest phenolic diversity was detected in bark (25), followed by leaves (18), peel (17) and finally, pulp (11). Three anthocyanins (cyanidin-3-O-galactoside > cyanidin-3-O-arabinoside > peonidin-3-O-galactoside) were determined in all ‘Baya Marisa’ tissues with their content highest in the peel. The innermost sections of the fruit were characterized by higher levels of dihydrochalcones and lower levels of most flavanols, flavonols and anthocyanins. These were predominant in the apple pulp nearest to the peel, with cyanidin-3-O-galactoside being the prevalent representative. Accumulation of anthocyanins in pulp is a rare trait in apples, and therefore, the distinct distribution and diversity of metabolites in this cultivar highlights its potential for high-nutrient products such as juices, apple chips or purees.