If you’ve ever tried making gluten-free bread or bagels, you probably noticed a big difference in texture compared to their gluten-packed counterparts. Traditional bagels get their chewy, firm texture from gluten—a protein found in wheat. But when you’re skipping gluten, you need a different approach to create that same structure.
Enter ingredients like flaxseed and chia! These power-packed seeds not only add nutritional benefits but also help give gluten-free bagels their shape and bite. Flaxseed and chia are rich in fiber and healthy fats, but more importantly for our bagels, they act as natural binding agents. This is a game-changer in gluten-free baking, where getting the right dough consistency is often tricky.
So, what makes these homemade gluten-free bagels unique? It’s the perfect combination of wholesome ingredients, proper techniques, and of course, flaxseed and chia. Let’s dive into the process to get your kitchen smelling like fresh-baked bagels in no time.
How Can You Achieve That Chewy Bagel Texture?
One of the biggest challenges in gluten-free baking is achieving the right texture. If you’re like most people, you want that perfect chew when you bite into a bagel, but gluten-free dough tends to be softer and more crumbly.
The key here is to replicate the binding and elasticity that gluten usually provides. That’s where the combination of flaxseed and chia comes in. These seeds absorb water and create a gel-like consistency, which helps hold everything together without making the dough too heavy. But it’s not just about adding seeds—you also need to get the dough texture just right.
For that iconic chewy bite, it’s important to boil your gluten-free bagels before baking them. This step creates a firm outer crust while keeping the inside soft and chewy. Just make sure you don’t skip this step if you want that authentic bagel feel!
Helpful Hint:
Let your bagel dough rest for 15 minutes before shaping it. This allows the chia and flaxseed to absorb moisture fully, making the dough easier to handle and shape.
What Ingredients Do You Need for Gluten-Free Bagels?
To make homemade gluten-free bagels, you don’t need a ton of fancy ingredients. The main stars here are gluten-free flour, flaxseed, and chia, but there are a few other essentials you’ll need to round out the recipe:
- Gluten-free flour blend (make sure it’s suitable for yeast baking)
- Ground flaxseed
- Chia seeds
- Instant yeast
- Warm water
- Sugar or maple syrup
- Salt
- Olive oil
These ingredients will give your bagels the flavor, structure, and slight crispness on the outside that you expect from a great bagel. The flaxseed and chia provide fiber, while the gluten-free flour does most of the heavy lifting when it comes to texture.
How to Make Homemade Gluten-Free Bagels
Now that you know what you need, let’s walk through the process of making these gluten-free bagels from scratch. Don’t worry, it’s simpler than you might think, and the reward is a batch of warm, homemade bagels that are perfect for breakfast or snacks.
Step-by-Step Guide to Making Gluten-Free Bagels
- Activate the yeast: Mix warm water, yeast, and a little sugar in a bowl. Let it sit for about 10 minutes until it becomes foamy.
- Mix the dry ingredients: In a separate bowl, combine your gluten-free flour, flaxseed, chia seeds, and salt.
- Combine the wet and dry ingredients: Add the activated yeast mixture to the dry ingredients, followed by a bit of olive oil. Mix until a sticky dough forms.
- Rest the dough: Cover the bowl with a clean towel and let the dough rest for 15 minutes. This allows the chia and flaxseed to absorb water and make the dough easier to handle.
- Shape the bagels: Divide the dough into equal pieces and roll each piece into a ball. Poke a hole in the center of each ball to form a bagel shape.
- Boil the bagels: In a large pot of boiling water, carefully drop the bagels in one at a time. Boil each side for about 30 seconds, then remove and place on a baking sheet.
- Bake: Preheat your oven to 425°F (220°C) and bake the bagels for 20–25 minutes until they turn golden brown.
Homemade Gluten-Free Bagels with Flaxseed and Chia
Prep Time: 25 minutes | Cook Time: 25 minutes | Total Time: 50 minutes

Ingredients
- 2 cups gluten-free flour blend
- 2 tbsp ground flaxseed
- 1 tbsp chia seeds
- 1 packet instant yeast
- 1 cup warm water
- 1 tbsp sugar
- 1 tsp salt
- 2 tbsp olive oil
Instructions
- In a small bowl, mix warm water, yeast, and sugar. Let sit for 10 minutes.
- Combine gluten-free flour, flaxseed, chia seeds, and salt in a large bowl.
- Stir in the yeast mixture and olive oil until a dough forms.
- Let the dough rest for 15 minutes, then shape into bagels.
- Boil the bagels for 30 seconds on each side, then bake at 425°F for 20–25 minutes.
What Are Some Fun Variations of Gluten-Free Bagels?
Once you’ve mastered the basic gluten-free bagel recipe, there are countless ways to mix things up and add some variety to your bagels. Whether you’re craving something sweet, savory, or a bit of both, there’s a flavor combo out there waiting for you. Here are a few ideas to get you started:
Sweet Cinnamon Raisin Bagels
To make a gluten-free cinnamon raisin version, simply add 2 teaspoons of cinnamon and 1/2 cup of raisins to your dry ingredients. This will give your bagels a hint of sweetness and spice, making them perfect for a breakfast treat. You can also sprinkle cinnamon sugar on top before baking for an extra touch.
Everything Bagels
If you’re a fan of savory bagels, you’ll love an “everything” version. After boiling the bagels, sprinkle them with a mix of sesame seeds, poppy seeds, dried onion flakes, dried garlic, and a pinch of salt. You can easily make this mix at home or buy an everything bagel seasoning blend from the store. Bake as usual, and enjoy that classic deli flavor!
Seeded Bagels with Flax, Chia, and Sunflower Seeds
For an extra crunchy and nutritious option, add a mix of seeds like sunflower, sesame, and pumpkin seeds to the top of your bagels before baking. This is a great way to boost the fiber and healthy fat content of your bagels, making them even more filling and satisfying. A sprinkle of sea salt on top pairs perfectly with the seed mix.
Helpful Hint:
When making sweet bagels like cinnamon raisin, keep an eye on the baking time. The added sugars from the raisins can cause the bagels to brown faster, so you may want to reduce the bake time by a few minutes.
How to Store and Reheat Gluten-Free Bagels
Freshly baked gluten-free bagels are best enjoyed warm, but it’s good to know how to store and reheat them for later. Like most gluten-free baked goods, these bagels can dry out faster than traditional ones, so proper storage is key to keeping them fresh.
Storing Bagels
Once your gluten-free bagels have cooled completely, store them in an airtight container at room temperature if you plan to eat them within a day or two. For longer storage, wrap the bagels individually in plastic wrap, then place them in a freezer-safe bag and freeze. They’ll keep in the freezer for up to three months.
Reheating Bagels
When you’re ready to enjoy a frozen bagel, simply let it thaw at room temperature for 15–20 minutes. To bring back that just-baked taste, pop the bagel in a toaster or oven for a few minutes until it’s heated through and slightly crispy on the outside. This quick reheat will give you a warm, chewy bagel every time.
What Toppings Pair Well with Gluten-Free Bagels?
One of the best things about homemade bagels is getting creative with the toppings! Whether you’re keeping it simple or going all out, there are endless options for customizing your gluten-free bagels to fit your cravings. Here are some tried-and-true ideas for topping your bagels:
- Classic Cream Cheese: You can never go wrong with a generous schmear of dairy-free cream cheese on your bagel. For added flavor, try adding chopped herbs or a sprinkle of garlic powder to the cream cheese.
- Avocado and Tomato: If you’re looking for a light and healthy option, top your bagel with mashed avocado, a sprinkle of sea salt, and sliced tomato. It’s a filling combo that’s perfect for breakfast or lunch.
- Peanut Butter and Banana: For a sweet and satisfying snack, spread peanut butter on your bagel and top with banana slices. A drizzle of honey (or agave) takes it to the next level.
- Smoked Salmon and Capers: If you want to go all out, spread your bagel with cream cheese, and top with smoked salmon, capers, and red onion. It’s the ultimate brunch bagel that’s both elegant and delicious.
Can You Make Gluten-Free Bagels Without Yeast?
While yeast is typically used in bagel recipes to help the dough rise, you can still make gluten-free bagels without it. Yeast-free bagels will have a slightly different texture—more dense and less chewy—but they can still be delicious. Here’s a quick alternative if you’re looking to skip the yeast:
Yeast-Free Gluten-Free Bagels
To make yeast-free gluten-free bagels, simply swap out the yeast for 2 teaspoons of baking powder. You’ll also want to increase the amount of warm water slightly to help activate the baking powder. Mix and shape the dough as usual, but instead of boiling the bagels, simply bake them straight away. They’ll rise a bit from the baking powder, but the texture will be more like a biscuit than a traditional bagel. It’s a great option when you’re short on time or ingredients!
Why Add Flaxseed and Chia to Your Bagels?
Both flaxseed and chia seeds offer a number of nutritional benefits that make them a perfect addition to homemade gluten-free bagels. These seeds are packed with fiber, omega-3 fatty acids, and antioxidants, making your bagels more nutritious and filling. Here’s why each ingredient is a standout in gluten-free baking:
Flaxseed Benefits
Flaxseeds are high in soluble fiber, which helps bind the dough and gives your bagels a more bread-like texture. They also have a nutty flavor that pairs well with savory and sweet toppings. Flaxseeds are also a great source of omega-3 fatty acids, which are beneficial for heart health.
Chia Seed Benefits
Chia seeds absorb liquid and form a gel-like substance, which makes them an excellent egg replacement in gluten-free baking. This gel helps to hold the dough together, preventing it from crumbling. Chia seeds are also rich in fiber, protein, and antioxidants, making your bagels more nutrient-dense.
Helpful Hint:
For a smoother texture, grind your flaxseeds and chia seeds before adding them to the dough. This will help them mix evenly throughout the dough and give you a more consistent result.
Flaxseed and Chia Nutritional Comparison
Nutrient | Flaxseed (1 tbsp) | Chia Seed (1 tbsp) |
---|---|---|
Calories | 37 | 58 |
Fiber | 2 grams | 5 grams |
Omega-3 Fatty Acids | 1.6 grams | 1.3 grams |
Protein | 1.3 grams | 2 grams |
Calcium | 26 mg | 76 mg |
Frequently Asked Questions
Wrapping Up
Homemade gluten-free bagels with flaxseed and chia offer the perfect combination of chewy texture, wholesome nutrition, and delicious flavor. Whether you’re new to gluten-free baking or a seasoned pro, this recipe brings you the satisfaction of fresh, homemade bagels without the gluten. The flaxseed and chia provide not only binding power but also a nutritional boost, making these bagels a great option for breakfast or a snack. Remember to follow the steps closely for best results and experiment with fun variations like cinnamon raisin or everything bagels. With the right techniques, you can enjoy bakery-style bagels right from your kitchen, anytime. Now it’s time to put your own spin on these bagels and share them with friends and family.