Panera Bread Apple Cinnamon Raisin Muffins

One of my favorite pastries at Panera is the apple cinnamon raisin muffin. Enormous, fluffy sweet muffins loaded with spiced apples, cinnamon, and raisins, topped with streusel and icing. What is not to love?

cinnamon apple raisin muffins with streusel topping and vanilla icing

Cinnamon Apple Muffins with Raisins

When I really love something from a restaurant, especially a chain restaurant that lists its menu ingredients online, I go over and try to figure out how to replicate my favorite as closely as possible. I am very pleased to say that I think I have done it with these muffins.

About This Apple Cinnamon Raisin Muffins Recipe

I will freely admit that this is not a beginner’s recipe. Although, if you have experience with making bread, you will definitely have a head start. There are a lot of components to this recipe: the bread base, cinnamon-raisin filling, spiced apple filling, streusel, and icing.

If you’re up for a day spent in the kitchen, enjoy it. You’ll be rewarded with the closest you can get to Panera without having to get in the car.

If you would rather not work quite so hard for your sweet Cobblestone reward, there are a few ways you can go about simplifying this recipe. I will make note of them at the end of the recipe.

Recipe Ingredients

I love Panera Bread, they have made a good effort in making sure their food has ingredients we can all spell and say simply. They are all about everyday food. It makes it easy for you to modify a recipe by changing out ingredients that work best for you.

Here’s a list of what you need for this recipe:

  • Butter
  • Sugar
  • Eggs
  • Kosher and table salt
  • All-purpose flour
  • Active dry yeast
  • Dark brown sugar
  • Honey
  • Ground cinnamon
  • Raisins
  • Apple pie filling
  • Cinnamon baking chips, optional
  • Powdered sugar
  • Vanilla extract
  • Lemon extract
  • Milk
  • Water

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 pieces into a jumbo muffin pan.
  9. Put apple filling on the pieces.
  10. Repeat with remaining dough pieces and apple filling so you have 3 layers of dough pieces and 2 layers of apple filling.
  11. Make the streusel topping and sprinkle it on top.
  12. Let rise then bake the muffins.
  13. Make the vanilla icing and drizzle it on the muffins.
cinnamon apple raisin muffins with crumb topping

Love Panera Bread? Look at these copycat recipes!

Favorite Sweet Breakfast and Bread Recipes

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.

Cobblestone Muffins

Panera Apple Cinnamon Raisin Muffins

Do you enjoy the Panera Bread Apple Cinnamon Raisin Muffins? Make them at home with this copycat recipe.
4.89 from 9 votes
Print Pin Rate Add to Collection
Course: Breakfast
Cuisine: American
Keyword: Apple Cinnamon Raisin Muffins, Panera Bread Cobblestone Muffins, Panera Bread Recipes
Prep Time: 30 minutes
Cook Time: 30 minutes
Total Time: 1 hour
Servings: 12
Calories: 651kcal


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


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.


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.


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

About Stephanie Manley

I recreate your favorite restaurant recipes, so you can prepare these dishes at home. I help you cook dinner, and serve up dishes you know your family will love. You can find most of the ingredients for all of the recipes in your local grocery store.

Stephanie is the author of's Dining Out in the Home, and's Dining Out in the Home 2.

REVEALED: Copycat Secrets for 2023

free email bonus

Yes, you CAN make it at home! I'll show you how.

We are a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for us to earn fees by linking to and affiliated sites.

Reader Interactions


  1. JeanneL

    5 stars
    I love Panera Bread’s Cobblestones but don’t live near one of their locations any longer so I have no access to them. So it was a delight to spot this recipe. I did make them and thought they were delicious. The only negative comment I have is they are huge. Of course I could have eaten only half of the muffin but it was so good I couldn’t stop. I think I will try the coffeecake you mention in the recipe next time. Or perhaps make them in standard size muffin tins. Otherwise I really enjoyed them and had a pleasant flashback to the days when I could get to Panera Bread shop.

  2. Christine

    4 stars
    I just made these. They are pretty good, and pretty close to panera’s cobblestone muffins. I did not stray from the recipe much except that I used apple pie spice instead of cinnamon and golden raisins. Per a different comment, Panera admitted that their cobblestone muffins were made with apple pie spice which makes sense. I liked them enough to make them again, but with some additional minor altercations. First, I think the dough needs a little more sugar. You do add the cinnamon raisin filling, but the dough still needs more sugar in my opinion because the dough itself tastes doughy. Also, I do not see the harm in adding a whole egg to the filling. It was tedious to whisk it and then try to take only half. I understand it’s a “binding agent” but it’s added to the filling with other sticky and bindable ingredients and then when you build the muffin you put spoonfuls of apple pie filling. The extra 1/2 egg split between 9 muffins is not going to affect the dough sticking together. The muffins were good, they were close to panera’s cobblestone muffins but not a perfect replica. I hope my comments help others make the perfect muffin. Thanks for sharing.

  3. Big Mike

    5 stars
    Maybe its a typo but if I cut 9 “cinnamon rolls” into 3 pcs I get 27 not 18.
    Im sure 3 per muffin is correct but then you only get 6 muffins.
    Also tried with golden raisins and dried apricots , good stuff. I also made a breakfast pudding type thing to spread the calories out.
    Thanks for figuring out this recipe especially since Panera has discontinued making them

  4. LENA

    I just went to my local Panera this morning to get a Cobblestone and didn’t see them in the case. When I asked, she said they discontinued them! I am so glad I found this recipe because life is just too short not to eat one of these every once in awhile. I will miss going to my local Panera (which to next to my favorite public library) and reading my new library finds while drinking a hot chocolate and snacking on one of these muffins on a cold day.

4.89 from 9 votes (4 ratings without comment)

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating

homemade Olive Garden Asiago Torgelloni Alfredo with chicken on a plate

Copycat Recipe Secrets for 2024


Yes, you CAN make it at home! 
I'll show you how.