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Preheat oven to 425F. Line a 6-count jumbo muffin tin, or 12-count regular muffin tin.
Reserve ½ cup of the chopped chocolate.
In a large mixing bowl, combine the flour, sugar, cocoa powder, baking soda, and salt. Mix well.
Make a well in the center to add the eggs, egg yolk, yogurt, olive oil, milk, and vanilla. Whisk the center until the eggs are beaten.
Switch to a spatula to fold the batter together just until combined (it’s okay if there’s still flour clumps).
Add the chopped chocolate and fold once more just until combined (and no more flour clumps).
Use a large ice cream scooper to divide the batter evenly between the muffin liners. Top with the reserved chocolate.
Bake for 5 minutes at 425F, then keep the oven door shut and reduce heat to 350F to cook an additional 15-20 minutes, until tops are set. A toothpick inserted into the center should come out clean or only with fine moist crumbs.
Remove muffins from the oven to cool in the pan 5 minutes, then transfer to a baking rack to cool another 10 minutes.
In the meantime, make the ganache by heating up the heavy cream just to boiling point. Pour over the chopped chocolate in a small bowl to sit for 5-10 minutes, whisk until smooth. Transfer to a piping bag to pipe about 1 tablespoon worth into the centers of each muffin.
Enjoy warm or let cool completely before storing.