Preserving the nutritional value of honey without compromising its properties until consumption is crucial. However, different types of honey may respond differently to packaging and storage conditions. This study aimed to assess the effects of different packaging materials (tin cans, light-colored glass jars, and dark-colored glass jars) and storage durations (initial, 6 months, and 12 months) on the physicochemical and antioxidant properties of pine, flower, and thyme honey. Nine samples were collected to conduct study on the three different types of honey. Honey samples were packaged in these materials and analyzed at the start, after 6 months, and after 12 months. The results showed that the moisture, proline content, sugar, total oxidant status (TOS), and oxidative stress index (OSI) levels were unaffected by honey type. Over time, there was a decrease in moisture, pH, proline content, diastase number, sugar, total phenolic content (TPC), total antioxidant status (TAS), and catalase activity, alongside an increase in the electrical conductivity, hydroxymethylfurfural (HMF), free acidity, TOS, and OSI levels. The packaging type did not influence the moisture, pH, electrical conductivity, proline content, diastase number, sugar, HMF, TPC, TAS, TOS, OSI, or catalase activity levels. The findings suggest that storing pine, flower, and thyme honey in light- or dark-colored glass jars or tin cans for 12 months does not significantly impact these properties. However, given the reduction in TPC and TAS across all honey types and packaging methods after 12 months, further studies are needed to explore ways to maintain honey quality in this regard.