Caatinga Biome fruits have been scarcely explored as a source of biotechnological yeasts. This study isolated yeasts from naturally fermented Caatinga fruits and evaluated Hanseniaspora opuntiae 125, Issatchenkia terricola 129, and Hanseniaspora opuntiae 148 on fermentation of soursop and umbu-cajá pulps. All strains were able to ferment the pulps (72 h), increasing (p < 0.05) acetic acid, phenolics concentration and bioaccessibility, and maintaining counts above 7 log CFU/mL after fermentation and/or in vitro digestion. H. opuntiae 125 showed the highest counts (8.43–8.76 log CFU/mL; p < 0.05) in pulps and, higher organic acids production, increased survival to digestion, and higher bioaccessibility of various phenolics (p < 0.05) in the umbu-cajá pulp. I. terricola 129 and H. opuntiae 148 showed higher metabolic activity, concentration and bioaccessibility of specific phenolics in umbu-cajá and soursop pulps, respectively (p < 0.05). Volatiles varied (p < 0.05) with the yeast strain. Generally, the yeast biotechnological performance for pulp fermentation was better on its fruit source.