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Preheat oven to 375.
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Line a muffin tin with paper or silicone muffin liners.
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In a large bowl, combine all wet ingredients until smooth. Set aside.
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In a small bowl, whisk together the coconut flour, baking soda, sea salt and pumpkin pie spice.
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Gently mix the dry ingredients into the wet until combined, then allow the muffin batter to rest for 5 minutes (this helps the coconut flour fully absorb the liquid).
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While letting the batter set, grind the pumpkin seeds briefly in a blender, food processor or spice grinder until roughly ground.
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In a small bowl, combine the ground pumpkin seeds with the softened butter, honey and pumpkin pie spice. Set aside.
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Portion out muffin batter into the prepared muffin tins, filling each muffin cup about 3/4 full with batter. Gently press the pumpkin seed topping into each muffin.
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Bake for 18-20 minutes, then allow to cool for a few minutes before popping the muffins out of the tray and placing on a wire rack to cool.