Name: Raspberry Cream Cheese Muffin Recipe
Prep time: 15 min
Cook time: 20 min
Total time: 35 min
Ingredients: 2 1/2 Cups Flour (fresh ground soft white wheat, all purpose, or a gluten-free blend.); 1/2 Teaspoon Baking Soda; 1 Teaspoon Baking Powder; 1 Cup Coconut Oil (or half and half butter and coconut oil); 1 Cup Sugar (I only use raw organic cane sugar to avoid GMO’s); 4 Whole Egg; 2 Teaspoons Vanilla; 2 Teaspoons Lemon Zest (grated); 1 1/2 Cups Plain Yogurt (or sour cream); 1/2 Cup Milk; 2 Cups Raspberries (fresh or frozen); 4 Tablespoons Cream Cheese (softened); 2 Tablespoons Sugar; 1 1/2 Tablespoons Fresh Lemon Juice; 1 Teaspoon Lemon Zest (grated); 1/2 Cup Powdered Sugar; 2 Tablespoons Lemon Juice

This recipe for raspberry cream cheese muffins has a hint of lemon and is super moist, thanks to the yogurt. You can swap out wheat flour for your favorite gluten-free blend, and try other variations like chocolate chip, blueberry, and more!

Hands holding a raspberry cream cheese muffin split in half to show the cream cheese filling.

Why You’ll Love This Recipe

A Taste of Summer Anytime – While I love making jams and jellies from our fresh fruit for later in the year, there’s nothing like fresh-baked goodies. Raspberry cream cheese muffins can be made with fresh or frozen berries, so you can enjoy them any time of year!
Make Ahead Convenience – Muffins make a quick breakfast or an on-the-go snack like my blueberry zucchini muffins, bakery-style double chocolate zucchini muffins, healthier pumpkin chocolate chip muffins, fresh (or frozen) peach muffins, and fresh cranberry muffins. But when our raspberries are coming on strong, these delicious gems need to be highlighted too.
Dessert Worthy – Due to the cream cheese filling and optional lemon glaze, these muffins are indulgent enough to make a sweet finish to any meal.

Why Raspberries Turn Green in Baked Goods

A woman holding a white bowl full of raspberries.

If your raspberry muffins look greenish around the berries, don’t worry. This is just because of a simple chemical reaction. The red pigments in raspberries change to greenish-blue when they meet baking powder.

This recipe uses lemon juice to help balance the acidity, so I haven’t had this problem, but if you do, you can try some of these tricks:

Reduce baking powder by ¼ teaspoon to lower alkalinity.
Use frozen raspberries—freezing lessens pigment reactivity.
Try a simple swap to help: mix half all-purpose flour with cake flour. Cake flour has less protein, which means a gentler baking environment.

Ingredients Needed

Raspberry cream cheese muffin ingredients: flour, sugar, baking soda, baking powder, coconut oil, lemon juice, lemon zest, vanilla, and raspberries.

A full ingredients list, including measurements, can be found in the recipe card below

Granulated Sugar – I prefer to avoid GMOs, so I use raw organic cane sugar.
Eggs – Learn how to store and preserve farm-fresh eggs here.
Vanilla Extract – Learn how to make vanilla extract here.
Raspberries – You can use fresh, frozen or freeze-dried raspberries for this recipe.
Unbleached All-purpose Flour – Fresh ground soft white wheat flour works wonderfully; see my post on grinding your own flour for baking tips when using freshly milled flour.
Cream Cheese – Make sure your cream cheese is softened to room temperature for even mixing.

Substitutions and Variations

Five white bowls filled with various gluten free flours.

I’m a firm believer in being resourceful and using healthy ingredient swaps in the kitchen, and this recipe is flexible to accommodate these ingredient substitutions.

Gluten-Free Flour Blend – You can use your favorite gluten-free flour blend to make this recipe gluten-free. Pro-Tip: Check out my tips for successful gluten-free baking here.
Coconut Oil – I like the taste butter lends to muffins, but prefer the texture achieved from the oil. When I use half of each, I get the best of both worlds.
Yogurt – Learn how to make homemade yogurt here. If you don’t have yogurt on hand, you can substitute sour cream.
Milk – For extra moisture, you can substitute homemade buttermilk.

Additionally, muffin recipes often provide plenty of wiggle room to customize for different seasons to make the best of other fresh fruits you may have on hand..

Spring/Summer – Toss in fresh blueberries for a vibrant muffin batter. Their tartness balances raspberries perfectly.
Autumn – Replace the raspberries with diced apples or pears. A pinch of cinnamon in the batter will warm things up without overpowering the fruit.
Winter – Replace the lemon juice, zest, and raspberries with orange juice, zest and fresh cranberries for a holiday appeal.
Anytime – Throw in a handful of chocolate chips or add a streusel topping for a sweeter, more dessert-like muffin.

How To Make Raspberry Cream Cheese Muffins

A hand holding a spoon mixing together flour, salt, baking soda, and baking powder.

Step 1: Preheat oven to 400°F. If you are not using muffin liners, grease muffin tins. Mix together flour, baking powder, and baking soda in a bowl and set aside.

An electric mixer whisking eggs, coconut oil, and sugar.

Step 2: In a medium bowl, cream together eggs, coconut oil, sugar and vanilla. Add in the yogurt, milk, and two teaspoons of the lemon zest.

A hand holding a spatula folding the wet and dry muffin ingredients together.

Step 3: Add the flour mixture to the wet ingredients and fold until just combined.

A hand holding a spatula folding raspberries into muffin batter.

Step 4: To prevent the raspberries from sinking to the bottom of the muffin, lightly dust them with flour. Then, gently fold the raspberries into the batter.

An electric mixer creaming together, cream cheese, lemon zest, and vanilla.

Step 5: Using the mixing bowl from your dry ingredients, cream together cream cheese, sugar, lemon juice, and remaining lemon zest.

Raspberry muffin batter and cream cheese filling in a muffin tin.

Step 6: Fill the muffin tins halfway with the batter, spoon a large teaspoon of the filling in the center, and top with the remaining batter to completely cover the filling.

Baked raspberry cream cheese muffins in a muffin tin.

Step 7: Bake in the oven for 16 to 20 minutes or until a toothpick inserted in the center comes out clean. The muffin top will be golden brown. Allow to cool completely.

A baked raspberry cream cheese muffin with a bite missing to show the cream cheese filling.

Step 8: Before serving, you can optionally top with a lemon glaze. Just whisk together powdered sugar with enough lemon juice to the desired consistency. Drizzle over the raspberry cream cheese muffins, and enjoy!

Storing and Freezing Instructions

Baked raspberry cream cheese muffins on a cooling rack.

Homemade muffins with fruit do not need to be refrigerated, but because this recipe has cream cheese, any leftover raspberry cream cheese muffins should be refrigerated or frozen.

First, allow the muffins to completely cool, then store them at room temperature in airtight containers for about 2-3 days (refrigeration dries out baked goods, so the muffins won’t stay fresh for very long.)

If you need to store your muffins longer, place cooled muffins in a single layer in a freezer-safe bag or container and freeze them for 3-4 months.

When you’re ready to thaw, simply remove the desired number of muffins from the freezer and let them thaw at room temperature.

Raspberry Cream Cheese Muffin Tips

A spoon drizzling lemon glaze over a raspberry cream cheese muffin.

Follow these muffin-making tips to achieve bakery-style muffins that are soft and moist with a tender crumb.

Detail	Tip
Prepare Your Raspberries	If using frozen berries, pat them dry and toss them with flour before folding them into the muffin batter. This will prevent sogginess and ensure even distribution. Fresh berries are much more delicate than frozen. To keep their shape, gently fold them into the batter.
Measuring	Use proper measuring utensils to accurately measure your ingredients, and spoon and level your flour instead of scooping it from the container. Using too much flour is the top reason muffins come out dense.
Mixing	Bring your wet ingredients to room temperature and mix your wet and dry ingredients separately before mixing them together. Don’t use an electric mixer when combining wet and dry ingredients. You could overdevelop the gluten, resulting in dense muffins or large holes in the crumb.
Filling	Do not overfill your muffin pan. Fill standard-sized muffin cups with about ¼ cup of batter; jumbo-sized muffins use about ½ cup batter per cup. Pro-Tip: Use a cookie scoop for ease of filling.
Baking	Don’t open the oven door before the minimum baking time is complete, or the muffins may deflate. To check if they are ready, insert a toothpick into the center of one muffin. If it comes out clean with no wet batter, they have finished baking.
Extras	Try some of the recipe variations above, or sprinkle a streusel topping for an added touch.