In apple processing, waste material known as apple pomace amounts to 45% of production volumes. When this residue is stored in open-air for its stabilization and potential uses, Volatile Organic Compounds (VOCs) are produced, resulting in environmental and odor pollution, and must be managed to avoid their impact. This work aims to study the emission of VOCs utilizing TD-GC/MS and its relationship with changes in physico-chemical (moisture, pH, proteins, among others) and biological (bacteria and fungi using Illumina MiSeq) parameters under three environmental conditions: open-air (outdoors), under-roof (indoors) and oxygen-free. The 8-month study results showed a gradual increase in odorous VOCs and microbial diversity, a product of chemical and biological transformation processes in the samples. A 30% increase in odorant compounds responsible for the unpleasant smell was observed, especially esters, aldehydes and hydrocarbons in samples stored in oxygen-free and Open-air conditions. Increases in VOCs over time were associated with changes in physico-chemical and biological parameters, as well as fluctuations in environmental variables (temperature, relative humidity, and precipitation). The results of this research allow establishing a relationship between storage conditions and the production of VOCs. In addition, recommendations for waste storage time are provided for the most common uses of apple pomace based on the physico-chemical parameters observed, in order to avoid the generation of odorous compounds. Of all storage methods analyzed, under-roof is the most adequate in practice. This study's findings are pertinent for managing agribusiness waste and its potential environmental pollution.