Copycat Panera Cobblestone Muffins

One of Panera’s most beloved pastries, the Cobblestone muffin stands as a testament to bakery perfection with its enormous, fluffy sweet base loaded with spiced apples, warm cinnamon, and plump raisins. These extraordinary muffins feature a delicate streusel topping and sweet vanilla icing that transforms an ordinary morning into something special. Now you can recreate this bakery favorite at home with this detailed copycat recipe that captures every layer of flavor and texture.

This post contains affiliate links. As an Amazon Associate, I earn from qualifying purchases.

What Makes This Recipe Special

When you genuinely love something from a restaurant, especially a chain that lists its ingredients online, the challenge becomes replicating that exact flavor and texture experience at home. These Panera Cobblestone muffins represent the pinnacle of bakery engineering, with multiple components working together to create something far greater than the sum of their parts. The result is a muffin that rivals anything you can buy, made with ingredients you can pronounce and customize to your preferences.

Recipe Ingredients

For the Bread Base:

• Butter – Creates rich flavor and tender crumb structure essential for bakery-quality results
• Sugar – Provides sweetness and helps develop a golden color during baking
• Eggs – Add structure, richness, and help create the characteristic fluffy texture
• All-purpose flour – Forms the foundation structure while maintaining a tender crumb
• Active dry yeast – Creates the light, airy texture that sets these apart from regular muffins

For the Cinnamon-Raisin Layer:

• Dark brown sugar – Contributes a deep molasses flavor and creates caramelized pockets
• Ground cinnamon – Provides warm spice that defines the signature flavor profile
• Raisins – Add chewy texture and concentrated sweetness throughout each bite

For the Apple Filling:

• Apple pie filling – Delivers tender spiced apple pieces with authentic bakery flavor
• Honey – Enhances natural apple sweetness and adds floral complexity
• Cinnamon baking chips (optional) – Provide extra cinnamon bursts and textural interest

For the Finishing Elements:

• Kosher salt and table salt – Enhance flavors and balance sweetness throughout
• Powdered sugar – Creates smooth, sweet icing for the final touch
• Vanilla extract – Adds aromatic depth to the icing
• Lemon extract – Brightens the icing with subtle citrus notes
• Milk and water – Provide proper consistency for dough and icing

How to Make Panera Apple Cinnamon Raisin Muffins

1. Make a simple bread dough for the muffin base.
2. Make a cinnamon mixture.
3. Make a cinnamon apple filling.
4. Roll out the dough into a rectangle.
5. Sprinkle cinnamon mixture and raisins on the dough.
6. Roll up the dough and cut it into slices.
7. Cut the slices into pieces.
8. Place a third of the pieces into a jumbo muffin pan.
9. Put the apple filling on the pieces.
10. Repeat this process with the remaining dough pieces and apple filling, creating 3 layers of dough pieces and 2 layers of apple filling.
11. Make the streusel topping and sprinkle it on top.
12. Let the muffins rise, then bake them.
13. Make the vanilla icing and drizzle it on the muffins.

Storage & Reheating Instructions

• Room Temperature Storage: Store in airtight containers for up to 3 days, maintaining optimal texture
• Refrigerator Storage: Keep for up to 1 week, though texture is best within the first few days
• Reheating Method: Warm in a 300°F oven for 5-8 minutes to restore just-baked texture and aroma
• Freezing: Wrap individually and freeze for up to 3 months, thaw at room temperature before reheating

Love Panera Bread? Look at these copycat recipes!

• Panera Black Bean Soup
• Panera Broccoli Cheddar Soup Recipe
• Panera Green Goddess Salad
• Panera Macaroni and Cheese
• Panera Tomato Soup

Favorite Sweet Breakfast and Bread Recipes

• Bread Machine Cinnamon Rolls
• Donut Muffins
• French Cruller Recipe
• How to Make French Toast Sticks
• Monkey Bread
• Oatmeal Muffins
• Starbucks Blueberry Muffin
• Starbucks Pumpkin Bread

Check out more of my easy bread recipes and the best Panera recipes here on CopyKat!

This recipe is from Jenni Field from the Online Pastry Chef, be sure to check out more of her recipes on her blog.

Panera Cobblestone Muffins Recipe

Fluffy apple cinnamon raisin muffins with streusel topping and icing. This Panera copycat recipe brings bakery favorites home!

4.89 from 9 votes

Print Pin Rate Add to Collection Go to Collections

Course: Breakfast

Cuisine: American

Keyword: Apple Cinnamon Raisin Muffins, Panera Bread Cobblestone Muffins, Panera Bread Recipes

Prep Time: 30 minutes minutes

Cook Time: 30 minutes minutes

Total Time: 1 hour hour

Servings: 12

Calories: 651kcal

Author: Stephanie Manley

Ingredients

For the Dough

• 1 cup water plus 2 tablespoons
• 1/4 cup butter melte
• 4 tablespoons sugar
• 1 large egg
• 1 teaspoon kosher salt
• 4 cups all purpose flour
• 2 teaspoons active dry yeast

Cinnamon Raisin Filling

• 1⁄4 cup butter softened, not melted
• 1⁄4 cup dark brown sugar packed
• 1⁄2 large egg (beat 1 large egg and then measure out half. Use the rest in your scrambled eggs)
• 2 teaspoons honey
• 1 tablespoon all-purpose flour
• 1 1/2 teaspoons ground cinnamon
• 1/4 teaspoon salt
• 1/4 cup raisins if you like more add an addition 1/4 cup

Spiced Apple Filling

• 1 cup apple pie filling Lucky Leaf brand recommended
• 1/4 cup cinnamon baking chips OR 1⁄2 teaspoon ground cinnamon
• 1/4 teaspoon salt

For the Streusel

• 1/2 cup all-purpose flour
• 1/2 cup granulated sugar
• 1/2 cup butter cool, should be softened
• 2 teaspoons honey
• 1/4 teaspoon ground cinnamon
• 1/4 teaspoon salt

For the Icing

• 1/2 cup powdered sugar
• 1/8 teaspoon salt
• 1/4 teaspoon vanilla extract
• 1/8 teaspoon lemon extract
• 2 teaspoons milk

Instructions

For the Dough

• Put the water, butter, sugar, egg, and salt in the bowl of your stand mixer. Stir briefly with a whisk. Add the flour, and then add the yeast on top. Mix on low speed with the dough hook until a shaggy dough forms, about 1 minute. Increase speed to medium and knead for 10 minutes. The dough will be soft, very shiny, and supple. It will also be very soft. Don’t worry about that–we want a soft dough. Leave the dough in the mixer bowl, and scrape it into a ball, spray with pan spray, and cover with plastic wrap. Let rise in a warm spot until doubled in size, about 1 1⁄2 hours. 

For the Cinnamon Raisin Filling

• Using a whisk or a hand mixer, mix all the ingredients except the raisins together until smooth. Reserve the raisins for assembly.

For the Spiced Apple Filling

• Using a chef knife, or a mini-prep, chop or pulse the apples until the pieces are about the size of small peas. You don’t want it completely smooth like applesauce. Think more like salsa. Stir in the salt and cinnamon chips, if using. If not using cinnamon chips, stir in the ground cinnamon and set aside. 

For the Streusel

• Using 2 forks, a pastry blender, or your fingers, mix all the streusel ingredients together until sandy with little clumps of butter. Set aside. 

To Assemble and Bake

• Sprinkle a bit of flour on top of the dough and then punch it down to press out the gases. Turn the dough out onto a lightly floured surface, and flour the top of the dough lightly as well. Roll dough into a rough rectangle about 18” x 10”. Spread the Cinnamon mixture evenly over the surface of the dough. Sprinkle on the raisins, if using. Starting from a long end, roll up the dough into a cylinder as if you were making cinnamon rolls. Pinch the seam to seal. Cut the dough into 9 equal pieces. Cut each of these pieces into 3 pieces for a total of 18 “cinnamon rolls.” 
• Line 2 jumbo muffin tins with jumbo muffin liners (you will only need to line 3 cavities in the second pan since this recipe makes 9 muffins). For each muffin, you’ll be using 3 of the “cinnamon rolls.” Cut the first in 4-5 pieces and put them in a lined muffin cavity. Top with a spoonful of apple filling. Repeat twice more with the second and third “cinnamon rolls.” When finished, you’ll have a muffin with 3 layers of cinnamon roll and 2 of spiced apple. You will be filling the muffin cups almost to the tops. 
• Continue making muffins with the rest of your dough and apple filling. Evenly sprinkle on the streusel, dividing it evenly among the 9 muffins. Cover muffins and let rise in a warm place until puffy, about 45 minutes. While muffins are rising, place a rack in the center of your oven, and preheat to 350 F. Bake until golden brown and well risen. The internal temperature of the muffins should be about 195F, give or take 5 degrees. This will take about 30 minutes. If the muffins seem to be browning too quickly, loosely tent with foil. Let the muffins cool for 10 minutes and then remove muffins to a rack to cool completely. Once cool, use a fork to drizzle each muffin lightly with the glaze.

For the Glaze

• Whisk the ingredients together until smooth. You can wait until the muffins are cooling after baking to do this part.

Notes

Ways To Simplify the Cobblestone Recipe

Start with store-bought sweet dough, such as the type made by Rhodes Bake-N-Serv. Instead of rolling out the dough and making “cinnamon rolls,” you can also roll the dough into ping pong ball-sized balls, dip them into the cinnamon mixture, and roll them in raisins. Use an equal number of balls for each muffin, making sure to add in the apple mixture. Leave out the apple mixture entirely. You can also leave off the streusel or the glaze if you prefer. Make a Cobblestone coffee cake by making the whole thing in a well-greased tube pan or springform pan.

Equipment

Mixing bowls

Muffin liners

Muffin tins

Nutrition

Calories: 651kcal | Carbohydrates: 92g | Protein: 7g | Fat: 29g | Saturated Fat: 17g | Cholesterol: 102mg | Sodium: 647mg | Potassium: 156mg | Fiber: 2g | Sugar: 46g | Vitamin A: 895IU | Vitamin C: 1mg | Calcium: 45mg | Iron: 2.8mg