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Preheat oven to 350 degrees Fahrenheit.
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Place the almond flour, salt, and baking soda in a medium sized bowl and mix.
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Grate in the frozen butter. Add the honey and using two forks, cut the butter and honey into the flour until the butter is incorporated into the flour.
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Add the vinegar and egg yolk and knead into the dough until there are no more yellow streaks.
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Separate into two balls, making one slightly larger than the other. Wrap in plastic wrap and place in the freezer for ten minutes.
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Core, peel, and slice the apples. Put in a large saucepan. Add the cinnamon, cloves, sea salt, lemon juice and zest, honey, and butter. Turn the heat onto medium and stir until everything is mixed together. Cook on medium heat for 15 to 20 minutes (stirring occasionally) or until the moisture is reduced.
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While the apples are cooking, roll out the smaller ball of dough in-between two layers of plastic wrap. Flip into an 8 or 9 inch pie tin.
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Place in the oven and bake for 8 to 10 minutes, or until it is a golden brown color. Take the crust out of the oven and let it cool.
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Fill with the cooked apples and place dabs of butter across the surface (about 1 tablespoon).
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Roll out the other ball of dough until it is slightly larger then the pie tin. Carefully place on top of the apple filling and flute the edges. Cut 4 small slices in the center, creating air vents.
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Reduce the heat of the oven to 325 degrees Fahrenheit. Place the pie in the oven for 30 to 35 minutes or until the crust is a nice golden brown color. Watch for burning along the edges and wrap foil along the edges to prevent burning if needed.