Hydroxymethylfurfural (HMF) is recognized as an undesirable component in honey and is usually formed as a result of heat treatment or prolonged storage of honey. HMF is formed as a result of chemical processes such as the Maillard reaction. Low levels of HMF are often associated with the freshness of honey. To prevent the formation of HMF in honey, it is thought that the application of the encapsulation process can increase the stability of this component and reduce its direct interaction. This method can help to extend the shelf life of honey and preserve its nutritional value. The protection provided by encapsulation may improve the overall quality of honey by reducing HMF formation depending on factors such as temperature and storage time. The aim of this study was to demonstrate that undesirable HMF formation can be prevented by encapsulating honey, which is rich in nutrients, with a biocompatible material. Accordingly, unencapsulated honey and encapsulated honey were kept in an oven at 80 °C for 2 hours and HMF formation was analyzed. In addition, the HMF content of unexposed honey, exposed honey and encapsulated honey samples were analyzed by high performance liquid chromatography (HPLC). As a result of the analysis, it was observed that the highest to the lowest amount of HMF was observed in honey exposed to temperature, encapsulated honey and honey samples not exposed to temperature, respectively. The calculated HMF amounts were 17.21 mg L^-1, 14.80 mg L^-1 and 14.70 mg L^-1, respectively. Furthermore, these results were supported by thermal gravimetric analysis (TGA) and Fourier transform infrared spectroscopy (FTIR). In conclusion, this study showed that the encapsulation method was effective in reducing HMF formation. The findings suggest that encapsulation can increase the stability of honey and therefore may be an effective method to extend its shelf life.