In this study, the synergistic effects of mixed-strain fermentation (Lacticaseibacillus rhamnosus GG, Lactobacillus acidophilus NCFM, and Bifidobacterium animalis subsp. lactis Bb-12) on enhancing the nutritional profile and volatile components of apple puree were investigated. Under the optimal fermentation conditions, the apple puree demonstrated significant improvements: (1) Nutritional enhancement: 62.78% and 29.48% elevation in total phenolics and total flavonoids, and antioxidant capacities improvement; (2) Sensory modification: the achievement of superior sensory score (92.44), reduced sweetness, and enhanced sourness and umami; (3) Volatile components: the identification of 91 volatile components, with increased concentrations of alcohols, esters, ketones and acids, and decreased concentration of aldehydes. Notable increases in key esters and alcohols such as 3-methyl-1-butanol (23.00%), ethyl acetate (47.17%) and γ-butyrolactone (14.67%) contributed to a fruity top note and long-lasting creamy fragrance. Decreases in acetaldehyde (10.03%), propanal (45.71%) and (E)-2-heptenal (39.08%) mitigated harsh spiciness and enhanced masked fruity for a more balanced flavor profile; (4) Simulated digestion: total phenolics remained stable in the gastric phase, but increased by 305.13% during intestinal digestion, which indicated improved bioaccessibility. Overall, this study demonstrates that mixed-strain fermentation enhances the nutritional value of apple puree and provides valuable insights into the fermented fruit and vegetable industry.