The objective of this study was to evaluate the antimicrobial effect of oregano essential oil and zeolite in solid state fermentation (SSF) of apple bagasse using 5% clinoptilolite zeolite (ZEO), oregano essential oil (0.1% OEO) and both additives (ZXA), compared against the traditional method including apple bagasse, urea, ammonium sulfate and mineral mix as control (CTL). The experiment included 3 replicates per treatment in laboratory plastic containers of 1 L, with sampling at 0, 6, 12, 24, 48, 72 and 96 h. Data were analyzed by repeated measures over time and multiple means comparison. Variables analyzed were aerobic mesophiic bacteria by plate count, pH with a potentiometer, and yeast count by improved Neubauer chamber. Results showed that maximum growth of yeast were obtained at 48 h in ZXA (462 × 10⁶ cells/g), while CTL achieved it at 96 h (470.5 × 10⁶ cells/g), thereby reducing the fermentation time and optimizing the process by the oregano extract antimicrobial activity and the capacity of the zeolite to regulate the concentration of nitrogen compounds. The count of aerobic mesophilic bacteria was decreased significantly (P < 0.01) at 48 h, from 0.70 × 10⁶ cfu/g in CTL to 0.25 × 10⁶ cfu/g in ZXA, being OEO the lower bacterial count treatment (0.11 × 10⁶ cfu/g). There was a higher pH (P < 0.01) in ZEO (4.80) and ZXA (4.62) versus CTL (4.06) and OEO (4.03), indicating that the adsorptive capacity of the zeolite allowed a slow and adequate release of the ammonia in the zeolite to the fermentation medium, resulting in a most efficient use of ammonia by yeasts, also regulating the pH and preventing volatile loss. We conclude that the use of both additives provides microbiological advantages over traditional SSF, reducing the fermentation time since yeasts have more available nitrogen compounds, and less foreign bacterial contamination, which could compete for substrates, production of secondary metabolites or modify pH. This guarantees a clean and free microbiological contaminants process.