Preheat oven to 350°F (175°C). Line a muffin tin with paper liners or grease well.
In a large bowl, whisk together the flour, cocoa powder, baking soda, baking powder, and sea salt until well combined.
In a separate bowl, whisk the eggs, then add the honey, cottage cheese, milk, vanilla, and sourdough discard. Mix until smooth.
Slowly pour in the melted butter, whisking constantly so it doesn’t solidify when it hits cooler ingredients.
Add the wet ingredients to the dry and gently fold together until just combined. Do not overmix.
Stir in the chocolate chips, reserving a handful for the tops.
Divide batter evenly between muffin cups, filling about ¾ full. Top each with a few extra chocolate chips.
Bake for 15–20 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs.
Let cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.