Heat oil in a wide pan and add French shallots. Let cook over a medium heat until shallots are starting to catch on the bottom of the pan. Add 1/2 tsp water and continue to cook until onions turn golden brown and caramelise. Set aside.
Mix almond meal, brown rice flour, arrowroot flour, bicarb soda, baking powder, flax eggs, water, coconut oil, and lemon zest and juice until lumps-free. Then add tomatoes, zucchini, basil, chives, sumac and beet powder and mix until combined. Make sure the zucchini is evenly mixed throughout the flour and not sticking together in clumps.
Evenly scoop mix into an oiled muffin tin. Bake in the oven for 20-30 minutes. Knife should come out clean and top crust should be golden brown. Let cool slightly then carefully remove muffins from tins with a spoon and place on a cooling rack until ready to eat.