Yeasts influence artisanal cheeses, affecting both flavour and spoilage. Nevertheless, their ecology, particularly in artisanal stretched-curd systems, remains poorly investigated. For such productions, the acidification process is often performed overnight on wooden tables, where members of the microbial consortia present in biofilms likely contribute to the fermentations. This study investigated two artisanal stretched-curd cheeses, namely Provola dei Nebrodi and Ragusano PDO cheeses, during different seasonal productions: spring-summer and winter, respectively. The impact of microbiota on both acidification and moulding wooden tables was compared with that on steel or plastic tables, respectively. Yeasts were enumerated using culture-based methods, and fungal communities were profiled by ITS amplicon sequencing. In Ragusano cheesemaking, yeasts increased by 2.7–2.9 log CFU g⁻¹ after acidification, reaching 5.46 log CFU g⁻¹ and 4.55 log CFU g⁻¹, on wood and steel tables, respectively. Conversely, in the Provola dei Nebrodi production, culture-based counts showed no differences.  In both cheese production, wooden tables were consistently dominated by Pichia spp. and Saccharomyces cerevisiae. After acidification, a material-specific selection was observed, with S. cerevisiae and Pichia enriched on wood with a season-dependent behaviour. Moreover, in wood-moulded cheeses, yeast values remained always higher than in plastic-moulded samples, with an observed divergence: cheeses moulded in wooden tables were richer in Pichia, whereas cheeses moulded in plastic tables were richer in Kluyveromyces lactis, Torulaspora quercuum, Kazachstania unispora, and Candida pseudoglaebosa. These findings delineate season and material-driven fungal communities and establish a baseline to evaluate their impact on quality, stability, and defect risk in artisanal practice.