Preheat oven to 375 degrees F and grease a 12-cup muffin tin with nonstick spray (or parchment liners).: As the oven warms, you may smell a faint warm scent from the heating elements, which is your cue that the environment is ready to bake. Greasing the tin or using liners prevents sticking and helps the muffin edges bake evenly. I preheat for at least 10 minutes to ensure steady heat, which encourages an even rise. A common mistake is skipping preheat, which can result in flat muffins, so always wait until the oven reaches the full temperature before placing the tin inside.
Add the flours, sugar, baking powder, baking soda, and salt to a medium bowl. Stir.: When you mix the dry ingredients, you distribute leaveners and salt evenly, ensuring a uniform rise and flavor. The combined dry mix should look homogenous, with the powders fully incorporated and no visible clumps of baking powder or soda. Stirring also awakens the flours so they blend readily with the wet ingredients. Avoid over mixing at this stage beyond combining, as doing so can develop gluten and make the muffins tough.
Stir the yogurt, butter, eggs, and vanilla in a separate bowl.: Whisking these wet components creates a smooth, slightly glossy mixture where the butter disperses through the yogurt . The aroma of vanilla will become noticeable, and the batter will look cohesive. Room temperature eggs whisk in more easily, reducing the chance of streaks. If you add very hot butter, it can cook the eggs, so be sure the butter is just warm and not piping hot.
Use a spatula to gradually fold the yogurt mixture into the flour mixture. Add the raspberries, lemon juice, and lemon zest and fold in to mix gently. (The batter will be thick.): Folding gradually prevents overworking the batter while allowing the dry ingredients to hydrate. The batter will be thick and slightly lumpy, which is desirable for tender muffins. When you fold in the raspberries , do so carefully so they stay intact and create pockets of fruit rather than turning the entire batter pink. You should see ribbons of batter and intact berries. A common error is vigorous stirring that bruises the berries and yields a uniformly colored batter rather than distinct fruit pockets.
Divide the batter among the prepared muffin tin, using about 1/4 cup batter in each cup.: Spoon or use an ice cream scoop for even portions so muffins bake uniformly. Each cup filled consistently leads to similar baking times and matching domes. As you fill, you may notice the batter slightly resist scooping because of its thickness, which is normal. If portions vary, some muffins will finish sooner than others; try to keep them equal to avoid uneven doneness.
Bake for 16-18 minutes, or until muffins are golden brown around the edges and a cake tester inserted into the center comes out cleanly.: During baking, the kitchen will be filled with a warm lemon berry scent and you should hear a subtle crackle as edges set. Golden edges and a springy top are visual cues of readiness. Insert a toothpick or cake tester into the center to check for crumbs rather than wet batter. Underbaked muffins will be dense and gummy, while overbaked ones dry out, so start checking at the lower end of the time range.
Let cool in the pan for a minute or so, then run a paring knife around the edges. Transfer to a wire rack and let cool fully.: Allowing a brief rest lets the muffins finish setting, which makes them easier to remove intact. Running a knife around the edges prevents tearing, and transferring to a wire rack helps prevent soggy bottoms by allowing air to circulate. You will notice a gentle release of steam as you move them, and the tops will firm slightly as they cool. A mistake here is leaving them too long in the pan, which can trap steam and soften the crust, or removing them too quickly and causing crumbling if they have not set enough.