Ever thought of apple pie stuffed bagels? Neither did I, until I tried stuffing my applesauce bagel dough with diced Honeycrisp apples. The sweet and tart apple pieces soften up nicely in the baking process and get all gooey with the cinnamon sugar they’re coated in. It’s a perfect filling and flavor combo for the fall, but also great treat to have year-round. Plus, because there are almost more apples in this bagel than bread, so it’s also kind of healthy and lower in calories than traditional bagels.

Here’s why I love this recipe
- No eggs, milk or butter and vegan friendly!
- Minimal kneading is required, and you don’t need to pre-cook the diced apple stuffing
- There’s a good source of nutrients and fiber, thanks to the applesauce in the dough, and the diced apples and cinnamon.

Ingredients Used to Make Apple Pie Stuffed Bagels
**I’ve linked some of these ingredients to amazon.com to give you an idea of what they are, but you should also be able to find them in your local grocery store (usually, the baking aisle, or the natural & organic food section). They are also affiliate links, which means that I earn a commission as an Amazon Associate if you decide to purchase the items. The price will be the same for you, link or no link 🙂
- Bread Flour – Bread flour is highly recommended for this recipe for the best texture and structure. TIP: For the best texture and chew, use a higher protein bread flour like King Arthur Bread Flour. Please read the note in the substitution section below if using other flours.
- Instant Yeast – you can find instant yeast in the baking section near the flours. My favorite is SAF Instant Premium Yeast, which works quickly and consistently produces great results. I recommend using instant yeast over active yeast for this recipe since active yeast needs to be activated in water.
- Sugar – I used raw cane sugar, but you can use regular granulated white sugar, or healthier alternatives like coconut, date, or maple sugars. Sugar-free substitutes such as monk fruit sweetener or stevia powder can be used in the filling, but for what goes inside the bread, I would NOT RECOMMEND using sugar-free substitutes since they can cause the bread to not rise properly.
- Salt – Pink Himalayan salt is what I have at home, so it’s what I use, but you can use any kind for this recipe.
- Applesauce – you can use any kind or any flavored applesauce. I used unsweetened.
Filling Ingredients
- Diced Honeycrisp Apples – sweet, tart and crispy, these Honeycrisp apples work so well in this recipe because they soften up perfectly without being overcooked inside the bagel. You can also use other apple pie apples like Granny Smith. Fuji is also one of my favorite apple pie apples.
- Cinnamon
- Brown Sugar
- All Purpose Flour – the secret of the apple pie filling in this recipe is actually AP Flour! The flour coats the cinnamon-sugar coated apple pieces and traps the apple juices inside the bagel and turns them into a delicious gooey sauce. I used AP flour, but bread flour will work just the same!
More Breakfast Recipes (HERE)
Step by Step Guide
How to Make Apple Pie Stuffed Bagels
STEP 1

In a clean mixing bowl, mix the dry ingredients: the bread flour, instant yeast, sugar and salt.
STEP 2

Add the applesauce, and use your hands or a danish dough whisk to combine it with the dry ingredients best you can.
STEP 3

*the bagel dough is supposed to be firm and somewhat stiff, since bagels require a lower water-to-flour-ratio. You can add additional 1-2 Tablespoons of water if there are still dry ingredients, but be sure to add one tablespoon at a time, so you don’t overhydrate the dough.
STEP 4

Loosely cover the dough with a clean wet towel or plastic wrap. Let rise, at a slightly warm place, for 60-90 minutes, until puffy.
After the first fermentation stage, choose ONE of two methods:
For no-knead (overnight) method: gently deflate the dough, and cover the bowl with plastic wrap loosely so that air can escape. Transfer the bowl to the fridge and chill overnight, at least for 8 hours and up to 48 hours.
For kneaded (quick) method: continue to knead the dough by hand or using a stand mixer, until the dough becomes smooth, supple, and pulls easily away from the bowl. The kneading should not take too long (about 3 minutes by hand) since we allowed the dough to relax and hydrate in the previous step.
STEP 5

Gently place the prepared dough onto a floured surface. If you chilled the dough in the fridge overnight, let the dough first come to room temperature (about 3-4 hours) before proceeding to the next step.
Shape the dough into a ball, and divide into 4 equal sized pieces
STEP 6

Mix the filling ingredients in a separate bowl
STEP 7

1. Use a rolling pin to roll out each piece of the bagel dough into a thin, 5 x 7 inch rectangle (thinner the better!)
2. Spread about 2-3 Tablespoons of the filling onto the bagel dough.
3-4. Roll the bagel dough over the filling.
5. Seal the ends by pinching the seams of the dough with wet fingers.
–> note: you can see in my photos that I had holes in my outer bagel dough and apple pieces poking out. This actually didn’t cause any problems! The moment the bagels hit the boiling water (next slide) the dough gets cooked and it seals up the filling inside.
6. Bring together the two ends of the bagel dough by inserting one end of the rolled dough into the other end.
7. Pinch the seams together so that they won’t fall apart during the boiling process.
8. Loosely cover the shaped bagels with plastic wrap or a clean wet paper towel. Let rise for 40-60 minutes, until the bagels look slightly puffed up.
STEP 8

Bring a pot of water to boil. Bring the heat down to medium-hot so that it’s gently boiling. Cook the bagel for just 30 seconds on each side.
TIP: If the bagel won’t float up to the surface by the end of the 60 seconds, it probably means the bagel needs to proof longer. I usually try this with one bagel first before cooking the other bagels in batches.
STEP 9

Bake the boiled bagels in the preheated oven for 20-25 minutes, until the tops are glossy and slightly browned.
STEP 10

Let the bagels cool before slicing. Enjoy!
Recipe Variations and Optional Add Ins:
Here are some awesome ways you can make this bagel recipe your own 🙂
- Add more flavor! Instead of cinnamon powder in the filling, add a pinch of ginger, cloves and nutmeg powder to bring out more of the fall flavors of this recipe. Also, you can add 1 tsp of vanilla extract to the dough ingredients enhance the sweet flavor.
- Add more texture! Adding chopped nuts, seeds, or dried fruits or oats is a fantastic way to increase the nutrition and flavor in breads, including this one. If you’re feeling indulgent, you can also add chopped candied pecans, or some granola in the filling. I tried adding walnut halves in mine (pic below!)

- Want to add more fiber? Substitute white whole wheat flour for up to half of the bread flour called for in this recipe. You’ll need to add a few more tablespoons of water to adjust the hydration since whole wheat flour absorbs more water than white flour.
- Go Unstuffed! If you prefer bagels without any stuffing you can always just make these bagels without any filling.
More Bagel Stuffing Ideas:
- Make these bagels healthier by adding a handful of nuts, seeds and old-fashioned oats to add texture and nutrition. Here are some ideas
- Nuts – chopped walnuts, pecans, cashews
- Seeds – poppy seeds, pumpkin seeds, sunflower seeds, sesame seeds, flaxseeds or chiaseeds
- Dried Fruit – chopped apricot, raisins, cranberries, dried cherries, candied ginger, citrus zests, etc.
Note on Substitutions
- Unfortunately, I haven’t tried making these with gluten-free flours, so I can’t recommend it as a substitute.
- If you don’t have bread flour, you can also use All Purpose Flour instead. AP flour has less protein than bread flour, so it will yield softer bagels with less chew/ bite.
How to Store
- For unstuffed bagels, you can store these bagels in an airtight container at room temperature for up to 3-4 days.
- For bagels with the apple pie filling, these bagels can be out at room temperature for a maximum of 2 days. For longer storage, you can place the bagels in a plastic freezer bag or airtight container and keep them in the fridge for up to 7 days, or in the freezer for up to 3 months. To reheat, toast inside an air fryer or toaster with the filling side up.
Final Tips for Stuffed Bagels
- Weigh your flour for the best results. 1 cup of bread flour = 120 grams / 4.23 oz. This is recommended since scooping the flour directly from the bag can pack the flour into the measuring cup, and this means you’ll end up with more flour than what’s called for in the recipe. If you don’t have a kitchen scale, you can measure the flour by spooning pre-sifted flour into the measuring cup, then using the straight end of the spoon to level the flour across the top to sweep off the excess.


Applesauce Bagels Stuffed With Apple Pie
Ingredients
Bagel Dough Ingredients
- 2 cup bread flour 240 g
- 2 tsp instant yeast 6 g
- 3 Tbsp sugar 37 g
- 1/2 tsp salt 3 g
- 6 oz unsweetened applesauce 170g , about 2/3 cup
Filling Ingredients
- 1 medium Honeycrisp apples , diced
- 1 Tbsp all purpose flour , or bread flour
- 1 Tbsp brown sugar
- 1 tsp cinnamon powder
Instructions
Combine the Dough Ingredients
- In a clean mixing bowl, mix the dry ingredients: the bread flour, instant yeast, sugar and salt.
- Add applesauce, using your hands or a danish dough whisk to incoporate it into the dry ingredients best you can.
- *the bagel dough is supposed to be firm and somewhat stiff, since bagels require a lower water-to-flour-ratio. You can add additional 1-2 Tablespoons of water if there are still dry ingredients, but be sure to add one tablespoon at a time, so you don’t overhydrate the dough.
- No kneading is required at this time. Loosely cover the dough with a clean wet towel or plastic wrap.
- Let rise, at a slightly warm place, for 60-90 minutes, until puffy.
After the First Rise (Choose ONE method below)
- For no-knead (overnight) method: gently deflate the dough, and cover the bowl with plastic wrap loosely so that air can escape. Transfer the bowl to the fridge and chill overnight, at least for 8 hours and up to 48 hours.
- For kneaded (quick) method: continue to knead the dough by hand or using a stand mixer, until the dough becomes smooth, supple, and pulls easily away from the bowl. The kneading should not take too long (about 3 minutes by hand) since we allowed the dough to relax and hydrate in the previous step.
Shaping the Dough
- Gently place the prepared dough onto a floured surface. If you chilled the dough in the fridge overnight, let the dough first come to room temperature (about 3-4 hours) before proceeding to the next step.
- Shape the dough into a ball, and divide into 4 equal sized pieces
Filling the Bagel Dough
- In a clean mixing bowl, mix the filling ingredients. Set aside.
- Use a rolling pin to roll out each piece of the bagel dough into a thin, 5 x 7 inch rectangle (thinner the better!)
- Spoon about 2-3 Tablespoons of the filling onto the bagel dough.TIP: For a thick cresent-shaped filling, place the filling towards one end of the rectangle. For a swirled effect, spread the filling throughout the dough so that it is evenly distributed.
- Roll the bagel dough over the filling, and seal the ends by pinching the seams of the dough. TIP: wet your fingers with some water to help with the sealing
- Bring together the two ends of the bagel dough by inserting one end of the rolled dough into the other end and pinching the seams together so that it won't fall apart during the boiling process.
- Place the stuffed bagels on a parchment lined baking pan, and loosely cover with plastic wrap or clean wet paper towel.
- Let rise for 40-60 minutes, until the bagels look slightly puffed up.
Boil the Bagels
- Bring a pot of water to boil. Bring the heat down to medium-hot so that it's gently boiling.Also, preheat the oven to 350F
- Use a wide slotted spoon or spatula to gently transfer 1 bagel into the water.
- Cook the bagel for just 30 seconds on each side. TIP: If the bagel won't float up to the surface by the end of the 60 seconds, it probably means the bagel needs to proof longer.
- Take the bagel out of the boiling water using a wide slotted spoon or spatula and back to the parchment lined baking sheet.
- Repeat the boiling process for the rest of the bagels.
Bake the Bagels
- Bake the boiled bagels in the preheated oven for 20-25 minutes, until the tops are glossy and slightly browned.
- Let cool to room temperature before serving. TIP: If slicing the bagels crosswise, you'll get the cleanest cut if the bagels (and the filling) are completely cooled.
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