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Preheat oven to 350F. Line a baking pan (8×8 or 9×9) with parchment paper. See notes for baking in ramekins.
In a large bowl, sift the flours together and then mix in the sugar, baking soda, salt, and baking powder. Set aside.
In another bowl, whisk eggs, vanilla, and milk then gently mix the egg-milk mixture in with the dry mixture. Stir until smooth or use a hand mixer to blend until batter is consistent texture.
Add the yogurt or applesauce, apple cider vinegar, spices to the bowl, and mix together.
Fold in the chopped/diced apple. If batter is too dry, add more milk.
Pour batter into lined baking dish. Optional thinly sliced apples on top. Set aside.
In a small bowl, mix melted butter and sugar. Add flour and stir until combined, making a crumble like texture. Spread over apple cake mix in pan. This will not cover the whole pan so feel free to double if desired.
Place in oven for 28 to 35 minutes (cover with foil after 20 minutes to prevent edges from browning). Bake until top is browned and flour is baked in center.
Once cooked, place on a towel in fridge for 20 minutes; this just helps it set. You can reheat again before serving, if desired. Or serve with yogurt or ice cream after it’s cooled.
Keep in refrigerator for 5-7 days or freeze in airtight container or ziplock for up to 3 months.