From Scientific American:

Honey’s ‘healing powers’ can be summarized into 5 main ingredients or activities of the components of honey;

1. Hydrogen peroxide – Honey contains an enzyme called glucose oxidase which breaks down glucose sugars and generates hydrogen peroxide, a kind of bleach, when there is free water available. In case you missed the antimicrobial component it was friggin BLEACH IN YOUR HONEY. I can feel you wondering why bees would bleach their own food supply and it turns out that is very simple. Any available water can cause the honey to spoil so the presence of glucose oxidase in the honey is an inbuilt anti-spoiling mechanism, pretty smart huh?

2. Sugar – The hydrogen peroxide control mechanism is a back up as very little free water exists in honey. The lack of free water is due to the vast amount of sugar dissolved into honey which gives it a low water activity. This essentially means that honey is more likely to take up water from its surroundings than have water removed from it and if you are a micro-organism it makes it very difficult to survive.

3. Methylglyoxal or MGO – This compound is an incredibly interesting and powerful antibacterial compound but, it is only found in certain natural honeys (Manuka honey from New Zealand) although it can be made in artificial greenhouses as well. This is the stuff that is making honey a potentially very useful topical salve (with the possibility of other forms of treatment being considered) in medical honey treatments such as MediHoney.

For more, see: You should rub honey on your everywhere