The present study sought to develop a headspace solid-phase microextraction (HS-SPME) gas chromatography-mass spectrometry (GC-MS) method to quantify free fatty acids (FFAs) and hexanal in cheese, and to track theirs levels over time. The developed method was applied on Fresh Asiago and Grana Padano cheeses, and FFAs and hexanal levels were monitored over 4 and 12 weeks respectively. Their evolutions were also compared from two types of packaging films: a high-density polyethylene (HDPE) package and a packaging bag named Ideabrill®. The later allowed a lower increase of these analytes (11.6-fold increase for Grana Padano and 5.9 for Fresh Asiago) compared to the HDPE packaging (21.5-fold increase for Grana Padano and 7.4 for Fresh Asiago). This method can contribute to the optimization of analytical methods in food industry for studies on shelf life, quality control or food packaging.