Savory Tomato Basil Muffins With Cheese

Imperial June 15, 2026June 15, 2026

Quick Recipe Version (TL;DR)

Yield: 12 standard muffins
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 40 minutes, including 5 minutes cooling in the pan

Quick Ingredients

2 cups all-purpose flour
1 tablespoon baking powder
1/4 teaspoon baking soda
1 teaspoon fine sea salt
1 teaspoon granulated sugar
1/2 teaspoon garlic powder
1/2 teaspoon freshly ground black pepper
2 large eggs
3/4 cup whole milk
1/2 cup plain Greek yogurt or sour cream
1/4 cup extra-virgin olive oil
1 cup seeded, finely chopped fresh tomato, drained and patted dry
1/3 cup thinly sliced fresh basil
3/4 cup finely shredded low-moisture mozzarella
1/4 cup finely grated Parmesan, plus 2 tablespoons for topping

Do This

1. Heat oven to 375°F and grease or line a 12-cup muffin pan.
2. Seed and chop the tomato, then drain it on paper towels so the muffins stay soft, not soggy.
3. Whisk flour, baking powder, baking soda, salt, sugar, garlic powder, and pepper in a large bowl.
4. Whisk eggs, milk, Greek yogurt, and olive oil in a second bowl until smooth.
5. Stir wet ingredients into dry ingredients just until barely combined, then fold in tomato, basil, mozzarella, and Parmesan.
6. Divide batter among muffin cups, sprinkle with the extra Parmesan, and bake for 18 to 22 minutes.
7. Cool in the pan for 5 minutes, then transfer to a rack and serve warm or at room temperature.

Why You’ll Love This Recipe

Soft, savory, and fragrant: These muffins are tender inside with bright tomato, fresh basil, olive oil, and a gentle cheesy finish.
Great with meals: Serve them alongside tomato soup, minestrone, salad, roasted vegetables, or a simple lunch board.
Easy pantry-friendly baking: No mixer is needed, and the batter comes together quickly in two bowls.
Mediterranean-style flavor: Tomato, basil, Parmesan, mozzarella, olive oil, and black pepper give these muffins a fresh, sunny taste.

Grocery List

Produce: 1 large ripe tomato, 1 bunch fresh basil
Dairy: 2 large eggs, whole milk, plain Greek yogurt or sour cream, low-moisture mozzarella, Parmesan cheese
Pantry: All-purpose flour, baking powder, baking soda, fine sea salt, granulated sugar, garlic powder, black pepper, extra-virgin olive oil, nonstick spray or paper muffin liners

Full Ingredients

For the Tomato Basil Muffin Batter

2 cups all-purpose flour, spooned and leveled, about 250 grams
1 tablespoon baking powder
1/4 teaspoon baking soda
1 teaspoon fine sea salt
1 teaspoon granulated sugar
1/2 teaspoon garlic powder
1/2 teaspoon freshly ground black pepper
2 large eggs, at room temperature if possible
3/4 cup whole milk, at room temperature if possible
1/2 cup plain Greek yogurt or sour cream
1/4 cup extra-virgin olive oil

For the Savory Mix-Ins

1 cup seeded, finely chopped fresh tomato, about 150 grams or 1 large ripe tomato
1/3 cup lightly packed fresh basil leaves, thinly sliced, about 12 grams
3/4 cup finely shredded low-moisture mozzarella, about 75 grams
1/4 cup finely grated Parmesan cheese, about 25 grams

For Topping

2 tablespoons finely grated Parmesan cheese
1 small pinch freshly ground black pepper, optional
1 tablespoon thinly sliced fresh basil for serving, optional

Savory Tomato Basil Muffins With Cheese – Closeup

Step-by-Step Instructions

Step 1: Heat the oven and prepare the muffin pan

Preheat the oven to 375°F. Lightly grease a standard 12-cup muffin pan with nonstick spray or line it with paper liners. If using paper liners, give the inside of the liners a very light spray as well; savory muffins can be a little more tender than sweet muffins and may cling when warm.

Step 2: Prep and drain the tomato

Cut the tomato in half across the middle and gently squeeze or scoop out the watery seeds. Finely chop the tomato until you have 1 cup. Spread the chopped tomato on a double layer of paper towels or a clean kitchen towel and let it sit for 5 minutes. Pat it dry well. This step is important because too much tomato juice can make the muffins heavy or gummy in the center.

Step 3: Mix the dry ingredients

In a large mixing bowl, whisk together the flour, baking powder, baking soda, salt, sugar, garlic powder, and black pepper. Whisk for about 20 seconds to distribute the leavening evenly, which helps every muffin rise nicely.

Step 4: Mix the wet ingredients

In a medium bowl, whisk the eggs until the yolks and whites are fully blended. Add the milk, Greek yogurt or sour cream, and olive oil. Whisk until smooth and creamy. A few tiny yogurt specks are fine, but the mixture should look mostly even.

Step 5: Combine the batter gently

Pour the wet ingredients into the dry ingredients. Using a flexible spatula or wooden spoon, fold the mixture together just until you no longer see large pockets of dry flour. The batter will be thick and slightly lumpy, which is exactly what you want. Avoid vigorous stirring, because overmixing can make the muffins tough instead of soft.

Step 6: Fold in the tomato, basil, and cheese

Add the drained chopped tomato, sliced basil, shredded mozzarella, and 1/4 cup Parmesan. Fold gently until the ingredients are evenly scattered through the batter. Try not to crush the tomato too much as you fold; keeping the pieces intact gives the muffins little juicy bursts of fresh flavor.

Step 7: Fill the muffin cups and add the topping

Divide the batter evenly among the 12 muffin cups, using about 1/4 cup batter per muffin. The cups should be about three-quarters full to nearly full. Sprinkle the tops with the remaining 2 tablespoons Parmesan and, if you like, a small pinch of black pepper.

Step 8: Bake until golden and set

Bake at 375°F for 18 to 22 minutes, or until the tops are lightly golden, the muffins spring back when gently pressed, and a toothpick inserted into the center comes out clean or with a few moist crumbs. If using an instant-read thermometer, the center of a muffin should read about 200°F to 205°F.

Step 9: Cool and serve

Let the muffins cool in the pan for 5 minutes. Run a small offset spatula or butter knife around any edges that stick, then transfer the muffins to a wire rack. Serve warm, at room temperature, or lightly reheated. For a pretty finish, scatter a little fresh basil over the muffins just before serving.

Pro Tips

Drain the tomato well: Fresh tomato adds flavor and color, but excess moisture is the main reason savory muffins turn dense. Seed it, chop it, and pat it dry.
Use low-moisture mozzarella: Fresh mozzarella releases too much liquid during baking. Low-moisture mozzarella gives the muffins a soft, cheesy texture without making them wet.
Do not overmix: Stir only until the batter comes together. A lumpy batter makes a more tender muffin.
Let them cool briefly: These muffins are delicate right out of the oven. Five minutes in the pan helps them set so they lift out cleanly.
Serve slightly warm: A quick reheat brings back the basil aroma and softens the cheese for the best texture.

Variations

Feta tomato basil muffins: Replace the mozzarella with 1/2 cup crumbled feta for a tangier, saltier Mediterranean flavor. Reduce the salt in the batter to 3/4 teaspoon.
Sun-dried tomato version: Replace 1/2 cup of the fresh tomato with 1/3 cup finely chopped oil-packed sun-dried tomatoes, patted dry, for a deeper tomato flavor.
Herby olive muffins: Add 1/4 cup finely chopped pitted Kalamata olives and reduce the salt to 3/4 teaspoon. This version is especially good with soup or a Greek-style salad.

Storage & Make-Ahead

Store cooled muffins in an airtight container at room temperature for up to 1 day or in the refrigerator for up to 4 days. Because they contain fresh tomato, refrigeration is best for longer storage. Reheat individual muffins in a 300°F oven for 8 to 10 minutes, or microwave one muffin for 15 to 20 seconds. To freeze, wrap cooled muffins individually and place them in a freezer-safe bag for up to 2 months. Thaw overnight in the refrigerator or reheat from frozen in a 300°F oven for 15 to 18 minutes. For make-ahead prep, you can chop and drain the tomato, grate the cheese, and whisk the dry ingredients up to 1 day in advance; mix the batter just before baking for the best rise.

Nutrition (per serving)