The effect of exotic fruit pulp (araçá, cagaita, cambuci, grumixama, blueberry, and uvaia) on probiotic viability during storage and after gastrointestinal tract (GIT) simulation, in vitro biological activity, total phenolics (TPC) and flavonoids content, and the production of metabolic products of microbial in probiotic yogurt were investigated. During the storage period (28 days), probiotic strain populations remained high (above 6 log CFU/g), while after the GTI simulation, L. acidophilus and B. animalis survival rates were higher when adding grumixama, blueberry, and uvaia pulp. Fermentation increased the antioxidant activity of yogurt containing araçá (12.87 ± 0.32 to 17.46 ± 1.79 μg Trolox/mg) and blueberry pulp (12.05 ± 1.43 to 17.49 ± 1.68 μg Trolox/mg) for ORACH for example. However, the total phenolic content increased in all samples after fermentation (ranging from 1.80 ± 0.26 μg gallic acid/mg (Uvaia) to 2.42 ± 0.08(Grumixama)), and there was no significant difference among treatments for total flavonoids. Thirty-eight metabolic compounds, mainly free amino acids, were detected, indicating a high degree of proteolysis in samples. Exotic fruit pulps positively impacted the probiotic yogurt parameters and are a potential alternative in functional food processing.