Heat and line. Heat a conventional oven to 375°F (190°C), with the rack in the middle. Line the twelve muffin cups and measure the chocolate chips separately. Let the oven finish preheating before the wet and dry mixtures are combined. Dark batter can disguise browned edges, so a correctly heated oven is more useful than relying only on color.

Whisk the cocoa mixture. Sift the cocoa into the larger bowl if lumpy. Add flour, sugar, baking powder, baking soda, and salt, then whisk thoroughly. Look for lighter streaks of flour around the bottom edge of the bowl and incorporate them now. This is the stage for thorough mixing; the finished batter needs a gentler approach.

Mix the wet ingredients. Whisk the eggs, yogurt, milk, oil, and vanilla in a second bowl. Continue until the oil is dispersed and large yogurt clumps are gone. The mixture does not need to become foamy. Keep the measured chocolate chips out of this bowl so they can be distributed when folding the batter.

Fold in the chocolate chips. Add the wet mixture to the dry ingredients and fold with broad strokes. When only a little flour remains visible, fold in the chips. Stop once the dry ingredients are incorporated; small soft lumps are fine. Divide among the twelve liners, keeping the portions similar so one oversized muffin does not dictate the baking time of the whole pan.

Bake and check between chips. Bake about 21–25 minutes. The tops should feel set and spring back gently. Insert a tester into the crumb of a center muffin, avoiding an obvious chocolate chip. Melted chocolate can leave a dark smear, but there should be no loose raw batter. If uncertain, check a second position rather than extending baking far beyond the needed time.

Release steam on a rack. Stand the pan on a heatproof surface for 5 minutes, then transfer the muffins to a wire rack for at least 10 minutes. The chips remain hot after the outside cools, so handle a broken muffin carefully. Wait until the batch is fully cool before wrapping for lunches or freezing.