Line a 12 hole muffin tin with paper cases and pre-heat your oven to 180℃ fan-forced.
Place the cheese (which has been cut into 3 cm pieces) into your Thermomix bowl and mix for 8 seconds, speed 8 to grate. Transfer to a new bowl and set aside until needed.
Without washing the bowl, place the zucchini (which has been cut into 3cm pieces) into your Thermomix bowl and mix for 5 seconds, speed 5.
Scrape down the sides of the bowl and add the self raising flour, onion flakes, ham (which has been torn into pieces) grated cheese, eggs, oil, milk and salt and pepper. Mix for 10 seconds, speed 5 on REVERSE.
Scrape down the sides of the bowl and mix for 5 seconds, speed 4 on REVERSE.
Divide the mixture between the paper muffin cases until they are around ⅔ full.
Finely dice the tomato and sprinkle on top of the muffins before placing them into the pre-heated oven to bake for 18 - 20 minutes or until cooked through when tested with a skewer.