In a small pot, melt the butter over low heat. Avoid burning it.
Set the melted butter aside to cool off.
Preheat the oven to 350° Fahrenheit or 180° Celsius.
In the meantime, using a whisk, mix the eggs, water, brown sugar, and cane sugar together.
Mix in the salt and whisk some more.
Add vanilla, nutmeg, and lemon zest, and continue whisking the ingredients.
While mixing the wet ingredients together, slowly pour in the melted butter.
Add yoghurt and milk, and give it a stir.
In a separate bowl combine flour, baking powder, baking soda, and using a spoon, mix them well together.
Add the cocoa powder, and continue mixing.
Combine the wet and dry ingredients by slowly adding the mixed flour with cocoa powder to the earlier mixed wet ingredients while gently stirring.
Add the chocolate chips and combine them with the muffin batter.
You can leave about ¼ cup of chocolate chips to place on top of the muffins.
Line a muffin pan with baking paper cups.
Pour about two scoops of the muffin batter into each cup. Just slightly beneath the rim, and sprinkle the extra chocolate chips on top.
Bake for about 22 - 25 minutes.