Preheat your oven to 200 degrees (fan-forced) and lightly grease 2 x 6 shallow cupcake trays.
Cut the cheddar and parmesan cheese into 3cm cubes and place into your Thermomix bowl. Grate for 10 seconds on speed 9 and transfer to a separate bowl until needed.
Without washing the bowl, add the zucchinis (which have been cut into 3 - 4cm pieces) and onion flakes and blitz for 4 seconds on speed 5. If you would like the zucchini to be grated smaller, blitz for another 2 seconds on speed 5.
Add the eggs, wholemeal flour, grated cheeses and salt and pepper and mix for 10 seconds on speed 4 reverse.
Scrape down the sides and mx for a further 10 seconds, speed 4 reverse to combine.
Divide the mixture between the trays and cook for 12 - 15 minutes or until golden.