It has been generally proven that the goaty flavor negatively affects consumer acceptance of goat milk (GM) products. In this study, the co-fermentation of isolated new yeasts with lactic acid bacteria (LAB) was applied to improve the aromatic properties of new fermented GM beverages. Microbial count, acidity, syneresis, water holding capacity, rheology characteristics, volatile compounds (VCs), and sensory characteristics were determined. Moreover, the obtained results of VCs were visualized using a heatmap with hierarchical cluster analysis (HCA) and principal component analysis (PCA). Theresults revealed that co-fermentation with Kluyveromyces marxianus strain K and SP-1 significantly increased the growth (9.74 ± 0.07 and 9.67 ± 0.11 log CFU/mL) and acid production (1.07± 0.05 and 1.06 ± 0.02%) of total LAB strains, respectively while enhancing the rheological properties. Results from SPME–GC–MS analysis showed that the relative content of hexanoic (4.62%), octanoic (3.08%), and decanoic (1.18%) acids which were associated with the goaty flavor decreased more in GYK (0.96, 1.09, and 0.38%) and GYS (1.30, 1.03, and 0.41%) beverages, respectively. HCA dendrogram showed that Candida ethanolica strain ATW-1 used to prepare GYA drinks was not adapting well in GM and was more similar to GY drinks. PCA bioplot showed that high content of acids, alcohols, and esters was generated throughout the fermentation. The inoculation of K. marxianus strain SP-1 into GM significantly improved FGM beverages aroma by reducing the goaty flavor and increasing the contents of total acids and alcohols thus, improving the FGM beverages by giving the balsamic, buttery, cheesy, and rosy flavors, with a little sweet taste. The study has positive prospects for the development of fermented GM with enhanced flavor for the beverage industry and other practical applications.