Line or spray 12 muffin tins and preheat your oven to 425℉.
In a small mixing bowl, add the cream cheese and 2 tbsp brown sugar. Mix vigourously with a spoon until well combined and smooth. Add in the 1/2 tbsp oat milk and 1/2 tsp vanilla extract and mix until combined. Set aside.
In a medium mixing bowl, add the flour, flaxseed, cocoa powder, baking powder and baking soda. Whisk until combined and set aside.
In a large mixing bowl, add the eggs and brown sugar. Whisk until well combined. Then add the oil, yogurt, oat milk, vinegar, vanilla extract and food colouring if using. Whisk until combined.
Add the dry mixture to the wet mixture and gently fold until just combined. Fill each muffin cup about 1/3 full. Then using a teaspoon, push down into the centre of the batter in each tin to create a little well. Spoon up a heaping tsp of cream cheese mixture and drop it into the little well. You may need a butter knife to help get the cream cheese out of the tsp. Repeat this for each tin.
Using the rest of the batter, fill each muffin tin to the top, ensuring the cream cheese is completely covered. This helps keep the cream cheese creamy and in the middle.
Bake at 425℉ for 5 minutes and then lower the temperature to 350℉ and bake for an additional 10-12 minutes or until the muffins spring back slightly when touched. Allow to cool in the pan for 5 minutes before transferring to a wire rack to fully cool. Store in an airtight container for up to 3 days or in the freezer for up to 3 months and enjoy!