We analyzed the red-fleshed apple cultivar ‘Baya Marisa’ and compared it with the traditional, white-fleshed apple cultivar ‘Golden Delicious’. The objective of this study was to compare sugars, organic acids, and phenolic compounds of ‘Baya Marisa’ with the widely known and consumed white-fleshed apple cultivar ‘Golden Delicious’. In addition, flesh firmness, color, and soluble solid content was studied. A total of 46 phenolic compounds were quantified and identified, some for the first time in apples. The study showed that the total analyzed phenolic content (TAPC) was 1.6× higher in the skin of red-fleshed ‘Baya Marisa’ and 1.4× higher in the flesh of red-fleshed ‘Baya Marisa’. Organic acid (citric acid, malic acid, and ascorbic acid) content was higher in the red-fleshed cultivar ‘Baya Marisa’, whereas sugar content (sucrose, glucose, and sorbitol) was similar, except for fructose, which was 1.1× higher in ‘Golden Delicious’. The content of citric acid was 1.6× higher in ‘Baya Marisa’, whereas the content of malic acid was 1.2× higher in ‘Baya Marisa’ and the content of ascorbic acid was 2.8× higher in ‘Baya Marisa’. Among phenolics, total dihydrochalcones in the skin were 3.3× higher in ‘Baya Marisa’ and similar in the flesh compared to ‘Golden Delicious’. Flavonols were 1.4× higher in the skin of ‘Baya Marisa’ and 2.8× higher in the flesh of ‘Golden Delicious’. Anthocyanins were not identified in the white-fleshed cultivar ‘Golden Delicious’. Total hydroxycinnamic acids were 2.0× higher in the skin of ‘Golden Delicious’ and similar in the flesh compared to ‘Baya Marisa’. Total flavanols were 1.8× higher in the skin and 2.2× higher in the flesh of the white-fleshed cultivar ‘Golden Delicious’.