Pre-heat the oven to 350 degrees and butter or coconut oil an 8x8 baking dish.
Make the pecan topping by using a fork to mix the topping ingredients in a bowl. Set this aside.
Blend the yogurt, coconut oil, eggs, honey, and almond extract in a medium mixing bowl until smooth and creamy.
Add the flours, baking powder, and salt, and blend until just combined.
Spread half of the coffee cake batter into your greased baking dish. Sprinkle half of the apples, gently press them down, and then sprinkle half of the pecan topping over the apples. Spread the other half of the batter over the apples, then put the other half of the apples and pecan topping on the batter. Use a butter knife to make swirls throughout the coffee cake.
Bake the coffee cake at 350 degrees for 40-45 minutes. Check your coffee cake around the 35 minute mark in case our ovens run differently – dark pans cook faster too. Let it cool 10 minutes before cutting and serving.