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It’s pumpkin spice season again, and what better way to celebrate than a lovely muffin?

My Pumpkin Muffins made with freshly milled spelt are perfect for any baker, but especially one learning the ropes of ancient grain baking. This recipe highlights warm fall spices and combines them with the nutrition and delicious natural flavor of spelt. I hope you try it!

Why Bake With Spelt?

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?

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.

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
• Kitchen scale (highly recommended)
• Measuring utensils
• Mixing utensil
• Muffin tin
• Muffin liners
• 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 Pumpkin Spelt Muffins

• Freshly milled spelt flour
• Baking powder
• Baking soda
• Salt
• Ground cinnamon
• Ground nutmeg
• Ground ginger
• Ground cloves
• Fresh or canned pumpkin puree
• Eggs
• Milk
• Brown sugar
• Neutral oil (I use refined coconut oil)

I tested this recipe for canned and fresh pumpkin puree. Canned pumpkin puree is consistently thick, whereas fresh pumpkin can vary quite a bit. I will include a measurement for canned and fresh, but I highly encourage you to look at my Step-by-Step section. Here you will find a better visual for what consistency you are trying to achieve in your spelt muffin batter.

Step-by-Step: How to Make Fresh-Milled Spelt Pumpkin Muffins

Step 1: Mill Your Grains

Mill your spelt wheat on a fine setting. If using coconut oil or butter, melt it and set aside to cool slightly.

Step 2: Mix Dry Ingredients

Mix your flour, salt, baking soda, baking powder, cinnamon, ginger, nutmeg, and cloves until combined.

Step 3: Mix Wet Ingredients

Mix your milk, pureed pumpkin, eggs, brown sugar, and neutral oil until well combined.

Step 4: Mix Wet Into Dry and Rest

Mix your wet ingredients into your dry and stir until no dry flour remains. Let rest for at least 15 minutes.

Preheat your oven to 375℉.

Step 5: Bake

Line your muffin tins with paper liners, or spray generously with oil. Use a 1/4-cup scoop to fill the tins.

Bake for 18-20 minutes or until a toothpick inserted into the center comes out clean. Let them cool slightly, then remove them and let them cool fully on a cooling rack.

Enjoy!

Fresh-Milled Spelt Pumpkin Muffins

• Prep Time: 15–20 minutes
• Bake Time: 18–20 minutes
• Yield: 12–13 muffins
• Oven: 375°F

Important: Gram measurements are best for the most consistent results, especially when baking with fresh-milled flour. Volume measurements are provided as estimates for convenience.

Ingredients

• 360 g freshly milled spelt flour (about 3 cups)
• 12 g baking powder (1 tablespoon)
• 3 g baking soda (½ teaspoon)
• 6 g salt (1 teaspoon)
• 2½ tsp ground cinnamon
• 1 tsp ground nutmeg
• 1 tsp ground ginger
• ¼ tsp ground cloves
• 175 g brown sugar (about ¾ cup + 1 tablespoon)
• 50 g neutral oil (about ¼ cup)
• 200 g pumpkin puree (about ¾ cup + 1 tablespoon)
• 2 large eggs
• 120 g whole milk if using fresh pumpkin (½ cup)
• 145 g whole milk if using canned pumpkin (about ½ cup + 1 tablespoon + 1 teaspoon)

Step 1 – Mill Your Flour

Finely mill the spelt on a fine setting. If using coconut oil or butter, melt and let cool slightly.

Step 2 – Mix the Dry Ingredients

Whisk together the freshly milled spelt flour, baking powder, baking soda, salt, cinnamon, nutmeg, ginger, and cloves.

Step 3 – Mix the Wet Ingredients

Whisk together the pumpkin, milk, eggs, brown sugar, and oil until well combined.

Step 4 – Combine and Rest

Stir the wet ingredients into the dry ingredients just until no dry flour remains. Let the batter rest for at least 15 minutes.

Step 5 – Bake

Preheat oven to 375°F. Line a muffin tin with paper liners or grease generously. Divide the batter between 12–13 muffin cups using a ¼-cup scoop.

Bake for 18–20 minutes, or until a toothpick inserted into the center comes out clean. Cool briefly in the pan, then transfer to a cooling rack to cool completely.

Pumpkin Puree Note

I tested this recipe with both canned and fresh pumpkin puree. Canned pumpkin is consistently thick, while fresh pumpkin can vary quite a bit in moisture. For this reason, the recipe uses slightly different amounts of milk for each.

I highly recommend checking the Step-by-Step section for a visual guide to the ideal muffin batter consistency, especially when using fresh pumpkin.

Tips for Success

• Mill your spelt on a fine setting
• Follow the gram measurements
• Try to mimic the batter consistency I have pictured in my Step-by-Step section
• Let your muffin batter rest for at least 15 minutes

Storage and Freezing Tips

I recommend storing any baked goods in a container like this bread bag, or a bread box would work well, too.

I think muffins are always best on the first day, but these muffins last well up to 3 days.

I love to freeze muffins! Let them cool fully, place in a labeled Ziploc bag, try to remove excess air, and seal. They last well up to 3 months.

FAQ

Can I use canned pumpkin instead of fresh pumpkin in these muffins?

Yes! I tested this recipe with both canned and fresh pumpkin. Canned pumpkin will give you more consistent results than fresh.

How should I store fresh-milled spelt pumpkin muffins?

I like to use a bread bag, but any lidded container will work fine.

Can I use another type of whole-grain flour instead of spelt?

You certainly can but this recipe is made specifically for spelt. I can’t guarantee that you will get the same results. I recommend adding the same, or slightly less, amount of milk and waiting 15 minutes for the bran and germ to absorb the liquid. If it seems too thick, feel free to add more liquid.

Spelt Pumpkin Muffins are a simple way to enjoy seasonal flavors. I hope that your family enjoys this recipe as much as mine has!

What’s your favorite way to enjoy a pumpkin muffin made with fresh-milled spelt flour?

Blessings,

Payton