Preheat your oven to 180°C (350°F) and line a 12-cup muffin pan with paper liners.
In a large bowl, whisk together the eggs, vegetable oil, vanilla extract, buttermilk, salt, sugar, sifted cocoa powder, and room-temperature Greek yogurt until smooth and well combined.
Sift the flour, baking powder, and baking soda directly into the wet mixture. Whisk or stir with a wooden spoon just until the flour mostly disappears. Do not overmix!
Add the chocolate chips and chocolate chunks. Use a rubber spatula to gently fold them into the batter until just combined.
Top with a few extra chocolate chips and bake for 18–20 minutes, or until a toothpick inserted into the center comes out clean. Let them cool in the pan for 15 minutes.
Place the chopped chocolate in a small bowl. Heat the heavy cream in a small saucepan over medium heat until it just begins to simmer, then pour it over the chocolate. Let it sit for 2 minutes, then whisk until smooth and glossy.
Core and Fill: Use an apple corer, a small knife, or the back of a large piping tip to cut a small hole about halfway down into the center of each cooled muffin.
Pipe or spoon the warm ganache directly into the centers until full. Let them set slightly and enjoy!
Notes
Don’t Core Too Deeply: When cutting out the center of the muffins, only go about halfway down. If you core all the way to the bottom, the liquid ganache will tear through the base and leak out of the paper liners.
Fill While the Ganache is Warm: Pipe or spoon the ganache while it is still warm and pourable. If it cools down too much and thickens, simply microwave it for 5–10 seconds to loosen it back up.
Use Room-Temperature Ingredients: Ensure your eggs, buttermilk, and Greek yogurt are at room temperature before mixing. Cold ingredients will cause the batter to seize, resulting in a dense muffin that doesn't rise well.
Avoid Overmixing: Stop mixing the exact moment the dry flour disappears. Over-whisking develops the gluten in the flour, which makes the muffins tough and rubbery instead of light and fluffy.
Measure Flour with a Spoon: Never scoop flour straight from the bag with your measuring cup. Fluff it with a spoon, gently spoon it into the cup, and level it off with the back of a knife to prevent adding too much dry flour.