Preheat the oven to 350°F. Line a muffin tin with parchment cups and lightly spray with non-stick spray if desired (helps prevent sticking).
In a medium mixing bowl, whisk together the almond flour, flax seeds, baking powder, and sea salt. Set aside.
In a large mixing bowl, whisk the eggs, maple syrup, vanilla, and milk until smooth. Add the peanut butter and whisk (or beat with a hand/stand mixer) until fully blended.
Add the dry ingredients to the wet ingredients and stir until well combined.
Fold in the chocolate chips.
Divide the batter evenly among the 12 muffin cups.
Bake for 18 - 20 minutes, until the muffins are lightly golden on top, domed, and a toothpick inserted in the center comes out clean.
Let muffins cool in the pan for 10-15 minutes.