Honey is a natural food with many unique properties. It has been used for millennia as an ingredient in food, beverages and medicine. Boiling honey changes some of its physical and chemical properties.
Some Flavor Is Lost
The flavours in honey are delicate and easily lost when cooked. A general rule of thumb is, "If it's too hot for your hand, it's too hot for your honey." Honey carries different flavours based on the plant from which it's derived. For example, honey made from orange blossoms will taste different than clover honey. When making products like mead, an alcoholic beverage made from honey, it is recommended not to boil the honey. Boiling is also unnecessary because honey has its own antimicrobial properties.
Some Enzymes Are Killed
All honey contains natural enzymes and bacteria. These microbes are what keep the honey from spoiling. Honey is the only food that will never go bad. When honey is boiled, the enzymes and bacteria within it are killed, leaving the honey vulnerable to spoiling.
The Honey Will Thicken
When you boil a syrupy substance like honey, some of the water contained in it will evaporate, leaving the remaining honey thicker than it was before. Boiled honey that has been allowed to cool will be more candy-like than syrupy. However, honey is hygroscopic, meaning it attracts water, so if left in the open, the honey will regain its moisture.
The Crystals Will Dissolve
Often an older jar of honey will separate, into a hard, white substance and some remaining liquid. This happens when the sugars in the honey form crystals (the hard, white part). This is normal -- the honey can still be used. If the jar of honey is placed in a hot or boiling water bath (not fully submerged), eventually the sugar crystals dissolve and the honey will become liquid again.