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Freshly baked muffins on a wooden surface, with one muffin in the foreground and several behind it.

Do you enjoy a muffin with coffee in the morning, but are trying to keep things lower in sugar? Are your kids carb-fiends, but you still want to feed them well?

Then you are in good company, friend! My family loves a good muffin, and I love to feed them well.

This Honey-Sweetened, Spelt Muffin is packed with nutrition from the bran and germ of fresh-milled spelt flour, yet perfectly sweet thanks to honey as a natural sweetener.

If you love the idea of a filling, healthy and perfectly sweet muffin for your family, then please read on!

Why Bake With Spelt?

Close-up view of scattered grains of wheat on a surface dusted with flour.

What Makes Spelt Different from Modern Wheat

Spelt, unlike modern wheat, has not undergone extensive hybridization (i.e., modification to improve yield and disease resistance). Spelt was modified with a domesticated wheat and a wild goat grass more than 4,000 years ago, but has been essentially unchanged since then.

This lack of tampering has kept its natural nutritional content and baking qualities.

Spelt Gluten Structure Explained

Spelt has a delicate but present gluten structure. Spelt wheat berries contain higher amounts of gliadins (stretch) but lower amounts of glutenins (strength) than modern wheat. This means that spelt dough can be stretched considerably, but will relax just as easily.

You can see this particularly in yeasted breads made of fully spelt. The dough will stretch far without tearing, but easily collapse or tear when baked.

Why Spelt Requires Gentle Mixing

While extensibility is not particularly important in a quick bread, like muffins, it is important to properly hydrate and handle spelt gently.

Spelt needs hydration suited to its particular needs as an ancient grain, along with light handling because its gluten structure breaks easily. I recommend folding ingredients until just combined, and then a 15-30 minute covered rest before baking.

If you’re new to fresh-milled baking, my Wheat Berry 101 post walks through what wheat berries are and what type of wheat is best for various baking applications.

Are 100% Spelt Muffins Healthier?

Freshly baked whole grain muffins on a wooden surface, with one muffin cut in half to reveal its soft, textured interior.

Fiber and Nutrient Profile

Spelt contains nutrition in volumes that modern wheat can’t quite compete with.

Spelt flour is naturally rich in fiber—much higher than modern wheat—and also provides notable amounts of protein, B-vitamins, and manganese. Because of its protective hull and high water solubility, spelt’s nutrients are easier for the body to access and stay stable for longer periods. Its vitamins and minerals are also more evenly distributed throughout the entire grain.

Honey vs Refined Sugar

Honey is an excellent choice when baking with spelt grains. Honey is hygroscopic, meaning it attracts and holds on to moisture well. This is particularly helpful when baking with spelt, as it has a tendency to dry out and crumble. Honey is acidic, which gently weakens gluten structure and creates a tender crumb. It also improves hydration without requiring excessive mixing.

Sugar is a perfectly acceptable choice, though it does not have honey’s naturally beneficial qualities. If you choose to swap the honey for sugar, you will need to increase the liquid in the recipe.

Who Spelt Is Best For (and Who Should Avoid It)

Spelt has been lauded as a more easily digestible grain, though this is truly based from person to person. Those with true wheat allergies should, of course, avoid it.

If you have had trouble with wheat in the past and are interested in trying out a fiber-rich grain that tends to have a gentler impact on blood sugar for some people, then spelt may be for you.

Check out my post on whole wheat nutrition to learn more about how whole grains support digestion, blood sugar balance, and overall nourishment.

Nutrition and grain background adapted and summarized from King Arthur Flour: Whole Grain Baking, First Edition (2006).

Tools You’ll Need

Grain mill
Mixing bowl
Measuring utensils
Mixing utensil
Muffin tin
Muffin liners
Kitchen scale (optional but recommended)
1/4 cup cookie scoop (optional, but man, does it make life easier)

If you’re just getting started with fresh-milled baking, I’ve rounded up my thoughts on grain mill shopping and everyday baking essentials in my post on top tools for fresh-milled baking.

Ingredients for 100% Spelt Muffins

Top view of various baking ingredients arranged on a checkered tablecloth, including a bowl of brown sugar, eggs, yogurt, and liquid ingredients.

Dry Ingredients

Fresh-milled spelt flour
Baking powder
Baking soda
Salt

Wet Ingredients

Honey
Neutral oil or melted, unsalted butter
Full-fat yogurt
Eggs
Milk

Optional Add-Ins (Fruit, Nuts, Spices)

You may add 50-100g of any add-ins your family loves. Think: chocolate chips, frozen berries, nuts or cinnamon. I would not exceed 1 1/2 tsp or 5 g of cinnamon, if you choose to add that.

Step-by-Step: How to Make Honey-Sweetened Spelt Muffins

Step 1 – Combine Wet Ingredients

A glass bowl containing three raw egg yolks, milk, and a whisk, with honey being poured into the mixture from a jar.

Let your yogurt, eggs and milk sit out until they are room temperature for best results.

Combine your neutral oil, or unsalted melted butter, with honey, yogurt, eggs and milk.

Step 2 – Incorporate Dry Ingredients

A glass bowl filled with a mixture of brown flour and baking powder, with a whisk resting inside, on a brown and white checkered tablecloth.

Combine your milled spelt flour, baking powder, baking soda and salt.

Combine your dry ingredients into your wet ingredients until no dry flour remains.

Step 3 – Resting the Batter (Optional but Recommended)

Muffin batter portioned into lined cupcake trays ready for baking.

Preheat your oven to 375°F.

Line your muffin tin with liners, or spray with oil.

Let your batter rest for 15-30 minutes, covered.

Scoop your batter into the muffin cups using a 1/4 cup cookie scoop or measuring cup.

Step 4 – Baking and Doneness Cues

Freshly baked cupcakes cooling in a muffin tin on a checkered cloth.

Bake for 18-22 minutes, or when a toothpick inserted into an innermost muffin comes out clean.

For the least amount of crumbling, be sure to let your muffins fully cool.

Enjoy!

Honey-Sweetened Spelt Muffins

Prep Time: 5 minutes
Rest Time: 20 minutes
Bake Time: 20 minutes
Yield: 12 muffins

Note: Gram measurements will give you the most consistent and reliable results, especially when working with fresh-milled flour. Volume measurements are provided as a convenience.

Ingredients

360 g fresh-milled spelt flour (about 3 cups)
150 g honey (about 1/2 cup)
60 g neutral oil or unsalted, melted butter (1/4 cup)
200 g full-fat yogurt (about 3/4 cup)
2 large eggs
80 g milk (about 1/3 cup)
12 g baking powder (1 tablespoon)
3 g baking soda (1/2 teaspoon)
6 g salt (1 teaspoon)

Optional add-ins: 50–100 g total (about 1/3–3/4 cup). Berries, diced apples with cinnamon, or chocolate chips work well.

Step 1 – Combine Wet Ingredients

Let your yogurt, eggs, and milk come to room temperature for best results.

Combine the honey, oil or melted butter, yogurt, eggs, and milk in a large bowl.

Step 2 – Incorporate Dry Ingredients

In a separate bowl, combine the spelt flour, baking powder, baking soda, and salt.

Add the dry ingredients to the wet ingredients and mix just until no dry flour remains.

Step 3 – Resting the Batter (Optional but Recommended)

Preheat the oven to 375°F.

Line a muffin tin with liners or grease well.

Cover the batter and allow it to rest for 15–30 minutes.

Scoop the batter evenly into the muffin cups using a 1/4 cup scoop or measuring cup.

Step 4 – Baking and Doneness Cues

Bake for 18–22 minutes, or until a toothpick inserted into the center comes out clean.

For the least amount of crumbling, allow the muffins to cool completely before serving.

Enjoy!

Common Spelt Muffin Problems and Fixes

Two freshly baked muffins stacked on a wooden surface, with a third muffin partially visible in the background.

Muffins Are Crumbly

This is a common issue when making muffins with fresh-milled flour. It is very important to let your muffins fully cool in order to achieve stability.

Also, it is crucial to let your batter rest before baking. This gives the bran and germ within the flour plenty of time to absorb liquids and soften.

Muffins Are Dense or Gummy

I highly suggest to always follow the gram measurements in any baked good, especially made with fresh-milled flour. Fresh-milled flour can vary greatly from grain to grain, so it is important to have exact measurements, rather than going off of highly variable cup measurements.

Muffins Didn’t Rise Well

It is very possible that you have over-mixed your batter. Spelt loses its gluten structure and liquid content very quickly. Once it is lost, it cannot be fixed. That is why it is important to mix until just combined.

Variations for Honey-Sweetened Spelt Muffins

Freshly baked muffins topped with blueberries and raspberries on a baking tray.

Blueberry Spelt Muffins

Add 50-100g of fresh or frozen blueberries. I highly recommend tossing the berries, lightly, in flour to prevent the berries from sinking in the batter.

Cinnamon Apple Spelt Muffins

Add 1 1/2 tsp (5 g) of cinnamon and up to 100 g of finely diced apples. I recommend lightly tossing the apples in flour to help prevent them from sinking in the batter.

Chocolate Chip Spelt Muffins

Add 50-100 g of your favorite chocolate chips. My family loves dark chocolate chips.

How to Store and Freeze Spelt Muffins

A freshly baked brown muffin sitting on a wooden cutting board.

Room Temperature Storage

Spelt muffins store well in covered storage for up to 3 days. I like to place them in a large, glass container with a lid for pretty display. Though, they never last more than a day!

Freezer Instructions

I love, love, love to have muffins in the freezer. It is a perfect thing to grab quickly when you need to run out of the house with nothing prepared. Often I like to take them to the park!

To freeze muffins:

Let cool fully
Place in a labeled zip-lock bag
Use a straw to suck out as much air as possible
And freeze!

Reheating Tips

I like to pop my frozen muffins in the microwave wrapped in a paper towel. This helps the muffins to not dry out. The time needed to thaw completely depends on the amount you are thawing and your microwave.

FAQ

Can I Use This Recipe With Sourdough Discard?

You can certainly try! I have not tested this recipe with sourdough discard, so you will likely need to adjust the liquid ratio. If you love fresh-milled sourdough muffins, then try out my recipe for Cinnamon Sugar Sourdough Muffins. It’s a family favorite!

Can I Make These Muffins Dairy-Free?

Absolutely. Just exchange the milk called for in the recipe for your favorite dairy-free milk, swap the yogurt for a dairy-free yogurt, and use oil instead of butter.

Can I Use Einkorn Instead of Spelt?

I have not tried this recipe with einkorn, but would venture to guess that it would work well. Einkorn is an ancient grain, like spelt, and does behave in somewhat similar ways. Let me know if it works well for you!