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The recovery of yeasts and lactic acid bacteria (LAB) involved in sourdough fermentation is the first step in the selection of starters with suitable technological aptitude and capable of producing desired aromas and/or aromatic precursors. In this work, two sourdoughs samples (MA and MB) and the derived doughs (samples A and B) were collected from a bakery during artisanal Panettone manufacture. Yeasts and bacteria were isolated at different fermentation steps on selective agar media. A total of 77 isolates were obtained and characterized. Representative strains of yeasts and LAB were identified by sequencing the D1/D2 domain of the 26S rRNA and the 16S rRNA genes, respectively. Moreover, the volatile organic compounds (VOCs) produced in the collected samples were detected and correlated to the species found in the same samples. The results highlighted the occurrence of <i>Kazachstania humilis</i> in both samples A and B, while <i>Saccharomyces cerevisiae</i> strains were detected only in samples B. Among LAB, <i>Fructilactobacillus sanfranciscensis</i> was the main species detected in both sourdoughs. Furthermore, strains belonging to the species <i>Lactiplantibacillus plantarum</i>, <i>Furfurilactobacillus rossiae</i>, <i>Lactobacillus parabuchneri</i>, <i>Leuconostoc citreum</i>, and <i>Leuconostoc mesenteroides</i> were assessed in the dough samples.