In a food processor, add oats and flax seeds. Pulse for 30-40 seconds until slightly ground. Preheat oven to 375°F.
In a separate large bowl, add flour, oats and flax seeds, baking powder and salt. Mix it using a whisk.
In a second large bowl, add eggs, olive oil, agave nectar, apple sauce and vanilla. Using a fork or a whisk, mix all wet ingredients until well combined.
Combine dry and wet ingredients. Fold in the chocolate chips. In a separate small bowl, add almond butter, cocoa powder and agave nectar. Mix everything with the fork well.
Line 10 muffin molds with parchment liners. Add one Tablespoon (about ⅓ full) of the dough in each muffin liner.
On top of the dough, add one teaspoon of chocolate almond butter. Fill the top of the muffins with more dough to cover the almond butter, until the muffin liner is about ¾ full.
Bake muffins for 23-25 minutes or until a toothpick comes out clear. Let the muffins cool down in a pan for 10 minutes before taking them out.