For long heather honey has been a special variety due to its unique organoleptic characteristics. This study aimed to characterize and optimize the isolation of the dominant volatile fraction of Greek autumn heather honey using solid-phase microextraction (SPME) followed by gas chromatography-mass spectrometry (GC-MS). The described approach pointed out 13 main volatile components more closely related to honey botanical origin, in terms of occurrence and relative abundance. These volatiles include phenolic compounds and norisoprenoids, with benzaldehyde, safranal and p-anisaldehyde present in higher amounts, while ethyl 4-methoxybenzoate is reported for the first time in honey. Then, an experimental design was developed based on five numeric factors and one categorical factor and evaluated the optimum conditions (temperature: 60 °C, equilibration time: 30 min extraction time: 15 min magnetic stirrer velocity: 100 rpm sample volume: 6 mL water: honey ratio: 1:3 (v/w)). Additionally, a validation test set reinforces the above methodology investigation. Honey is very complex and variable with respect to its volatile components given the high diversity of the floral source. As a result, customizing the isolation parameters for each honey is a good approach for streamlining the isolation volatile compounds. This study could provide a good basis for future recognition of monofloral autumn heather honey.