If you have a soft spot for breakfast treats that feel like a warm hug, you are going to fall head over heels for this Apple Cream Cheese Stuffed Bagel Bites Recipe. Imagine tender, fluffy bagel dough enveloping a luscious, roasted apple and smooth cream cheese filling that bursts with cinnamon sweetness in every bite. These bagel bites are not only a feast for the taste buds but also a fun project that will fill your kitchen with mouthwatering aromas. Whether you’re looking to impress brunch guests or treat yourself to something special, these little delights will become your new go-to comfort food.

Ingredients You’ll Need

The image shows several fresh apples on a wooden surface with a white marbled texture background. There are three whole apples with shiny red and yellow skin, each showing a greenish stem area. Alongside them, there are apple slices: two halves showing the white inside with seeds and core visible, and three thinner wedge slices arranged nearby. The skin of the apples remains bright red on the outside, while the inside is a light cream color. The view is from above, showing the apples and slices spread out comfortably in the frame. Photo taken with an iphone --ar 4:5 --v 7

Simple ingredients that are easy to find but come together to create a magic combo of flavors and textures. Each one adds something important: sweetness, spice, creaminess, and that perfect bagel chew.

2 apples, peeled and chopped into 1″ chunks: The star of the filling, providing natural sweetness and tender fruit texture.
¼ cup plus 1 tablespoon brown sugar: Adds rich caramel notes to the roasted apples and balances the cream cheese’s tang.
½ teaspoon cinnamon: Warms the filling with classic spice without overpowering the fresh apple flavor.
1 tablespoon butter: Adds luscious richness to the roasted apples.
8 ounces cream cheese, softened: The creamy base that mingles perfectly with the fruit for a luscious filling.
1 teaspoon vanilla extract: Sweetens and deepens the filling’s flavor beautifully.
2 teaspoons active dry yeast: Essential for that fluffy, chewy bagel dough.
1 ¼ cup plus 1 tablespoon warm water: Activates yeast and hydrates flour for the dough.
1 tablespoon honey: Natural sweetener that helps the dough rise and adds subtle sweetness.
3 ½ cups bread flour: Provides structure and chewiness to the bagels.
2 tablespoons granulated sugar: Brings balance to the dough alongside the honey.
1 ½ teaspoons salt: Enhances the flavors in the dough.
1 teaspoon cinnamon: Adds a gentle warmth to the dough itself, echoing the filling’s spice.
2 quarts water: For boiling bagel bites to get that classic shiny crust.
Additional honey and sugar for boiling water: These add flavor and help achieve the perfect bagel crust.
Egg wash (1 egg beaten with 1 tablespoon water): For that gorgeous golden finish and to help the cinnamon sugar stick.

How to Make Apple Cream Cheese Stuffed Bagel Bites Recipe

Step 1: Roast the Apples

Start by tossing those fresh apple chunks with a tablespoon of brown sugar and cinnamon, then spread them onto a baking sheet dotted with butter pieces. Roasting at 400 degrees creates a sweet, fragrant mixture that softens the apples while concentrating their flavor. The roasting process transforms ordinary apples into tender jewels that become the heart of your filling. Let them cool completely before mixing to avoid melting the cream cheese.

Step 2: Prepare the Cream Cheese Filling

While the apples cool, beat softened cream cheese with the remaining brown sugar and vanilla extract until silky smooth. This step is key for achieving a perfectly sweet and creamy filling that contrasts wonderfully with the warm, spiced apples. Once smooth, gently fold in the roasted apples to keep that lovely texture intact. Portion the filling into roughly 20 tablespoon-sized balls and pop them into the freezer until you’re ready to assemble, ensuring they hold their shape in the bagel dough.

Step 3: Mix and Knead the Dough

Activate your yeast in warm water with honey, watching it foam to know it’s alive and kicking. Add this mixture to your stand mixer bowl along with bread flour, sugar, salt, and cinnamon. Knead the dough for 7-8 minutes until smooth and elastic, then allow it to rest under a cover for 45 minutes so it can double in size. This resting period is where the magic happens—air bubbles expand, giving you that airy bagel texture everyone loves.

Step 4: Shape Bagel Bites with Filling

After punching down the rested dough, divide it into 20 equal pieces and roll each into a ball. Flatten each into a 4-inch circle and place a frozen ball of apple cream cheese filling in the center. Carefully pull the dough edges up and around, sealing the filling inside like a luscious secret pocket. Gently roll filled dough balls into smooth spheres and arrange them on parchment-lined baking sheets. A short 20-minute rest lets the dough relax and puff slightly before boiling.

Step 5: Boil the Bagel Bites

Bring water to a rolling boil with honey, then carefully drop a few bagel bites in at a time. Boil each batch for about 15-20 seconds—this step is crucial to develop that classic bagel crust and chewy texture. Using a slotted spoon, transfer bagel bites back to the baking sheets. Boiling these bite-sized bagels before baking gives you that satisfying crust to crisp up alongside a tender interior.

Step 6: Add Cinnamon Sugar Topping and Bake

Brush the boiled bagel bites with egg wash to help them develop a shiny, golden crust. Sprinkle generously with a homemade cinnamon sugar mix for a sweet and spicy finish that perfectly complements the filling. Bake the bagel bites in a 325-degree oven for 25-30 minutes until beautifully browned. Let them cool slightly so the filling firms up just enough for handling, but not so much you lose that warm, gooey appeal.

How to Serve Apple Cream Cheese Stuffed Bagel Bites Recipe

A close-up of six round baked buns with a golden-brown crust sprinkled with cinnamon. One bun is shown cut open, revealing a soft, light beige bread layer wrapped around a filling of chunky, light brown apple pieces mixed with creamy cinnamon-spiced filling inside. The buns are placed on a piece of parchment paper on a wooden surface, with two cinnamon sticks positioned near the bottom right corner. In the background, there is a red apple slightly out of focus. Photo taken with an iphone --ar 4:5 --v 7

Garnishes

Few things elevate these bagel bites like a light dusting of powdered sugar, a drizzle of honey, or even a pinch of freshly ground cinnamon on top. Fresh apple slices or a dollop of extra cream cheese on the side make beautiful garnishes that hint at the flavors inside and add visual appeal. These garnishes add an extra layer of sweetness and texture that make every bite feel special.

Side Dishes

Serve alongside fresh fruit salad or a crisp green salad for a well-rounded breakfast or brunch. A warming mug of chai tea or a spiced latte pairs beautifully with the cinnamon notes in the bagel bites, creating a cozy and satisfying meal. The contrast of cool, fresh fruit against the warm, creamy bagel bites keeps the palate refreshed and happy.

Creative Ways to Present

Arrange the bagel bites on a wooden board or tiered stand for a charming brunch spread that invites friends to dig in. You can also serve them skewered with toothpicks as bite-sized party snacks or pack them alongside coffee for a delicious on-the-go treat. Playing with presentation makes enjoying this Apple Cream Cheese Stuffed Bagel Bites Recipe even more fun and inviting for your guests or family.

Make Ahead and Storage

Storing Leftovers

These stuffed bagel bites keep beautifully at room temperature for a few hours, but for longer freshness, store them in an airtight container in the refrigerator. They stay moist and tasty for up to three days, making them perfect for quick breakfasts or snacks throughout the week.

Freezing

If you want to prep ahead, freeze unbaked bagel bites after shaping and before boiling by placing them on a baking sheet until firm, then transferring to a freezer bag. You can also freeze fully baked bagel bites once cooled for up to a month. This way, you have a ready stash of warm, comforting bites whenever you crave them.

Reheating

To reheat, warm in a preheated oven at 350 degrees for about 10 minutes until heated through and crispy again. Avoid microwaving to keep that perfect texture. You can also toast them lightly before serving to revive their bakery-fresh charm.

FAQs

Can I use other types of apples for the filling?

Absolutely! Crisp apples like Granny Smith or Honeycrisp work best because they hold their shape well when roasted and provide a nice balance of tartness and sweetness.

Is there a substitute for cream cheese?

You could try mascarpone or ricotta for a milder flavor and looser texture, but cream cheese’s tanginess really compliments the apples, so it’s the ideal choice to keep the flavors balanced.

Can I make these bagel bites gluten-free?

With some experimentation using gluten-free bread flour blends, you might get close, but traditional bread flour is key to achieving that chewy, authentic bagel texture.

What is the purpose of boiling the bagel bites before baking?

Boiling sets the crust and gives the bagels that classic shiny, chewy exterior you expect. Skipping this step results in a softer, less bagel-like texture.

How long can I store these bagel bites after baking?

They are best eaten within 2-3 days if refrigerated. Beyond that, their texture and flavor start to diminish, so enjoy them fresh or freeze extras for future enjoyment.

Final Thoughts

There’s something so heartwarming about baking up a batch of these Apple Cream Cheese Stuffed Bagel Bites Recipe—they combine familiar fall flavors with the fun of homemade bagels, creating a snack that’s both nostalgic and new. If you adore sweet and spicy comfort food that feels lovingly crafted, I can’t recommend this recipe enough. Grab your apron, get ready to fill your kitchen with irresistible cinnamon-apple aromas, and treat yourself to a batch of these delightful bites—you deserve it!