The addition of organic green banana flour (GBF, 0%, 1%, 3%, or 5% w/v) on the quality parameters of fermented milk was investigated (21 days/5 °C). Suitable viability of lactic and probiotic cultures (>6 log CFU/g) and resistant starch level (3.01–10.29 g/100 g) were observed. 1% and 3% GBF addition increased post acidification, proteolysis and concentration of lactic and acetic acids, but at suitable ranges. Furthermore, it improved the fatty acid (long-chain) and volatile profiles, increasing aroma and flavor acceptance. 3% GBF addition resulted in higher firmness, lower atherogenic and thrombogenic indices and better aromatic profile than 1%, allowing the consumption of lower quantities of the fermented milk (100 g) to provide the minimum daily intake of resistant starch. GBF at 3% is a suitable ingredient in fermented milk formulation, contributing to the development of a synbiotic product with shelf life of at least 21 days.