Preheat the oven to 375 degrees. Grease a 9 inch springform pan.
Make the Apple Topping: Add the chopped apples to a glass baking dish (8x10 or 9x13 would work). Sprinkle the lemon juice and vanilla extract over the apples. Add the flour, cinnamon, nutmeg, and salt to a small bowl or cup to combine, then sprinkle over the apples. Drizzle honey over the apples. Toss it all together. Cook the apples for 20 minutes while preparing the cake.
Make the Honey Cake: Using a stand mixer with a paddle attachment or an electric hand mixer, beat the butter and honey together until fully combined. Add eggs one at a time and mix until combined, then the yogurt and vanilla and mix until combined.
Add the dry ingredients to the top and lightly mix the dry ingredients together before folding into the batter. Pour the batter into the springform pan.
Once the apples have cooked for 20 minutes, lower the heat to 350 degrees. Add the cake to the middle rack, apples to the top rack.
Cook for 30-40 minutes, or until the cake is no longer wobbly and a toothpick inserted in the center comes out clean. Check on the apples. They should be soft but not burnt.
Take the cake out and allow to cool for 5 minutes. Scoop the apples over the cooled cake.