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Einkorn Apple Cinnamon Muffins (Naturally Sweetened)

These cozy Apple Cinnamon Muffins are made with wholesome einkorn flour, naturally sweetened with pure maple syrup, and filled with fresh grated apples for a tender, flavorful crumb. Each muffin is finished with a crunchy walnut cinnamon-sugar topping that adds the perfect touch of warmth and texture — a comforting fall treat you’ll want to bake all year long.

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Why you'll love these naturally sweetened muffins

Nutrient-Rich: Einkorn is an ancient grain known for its high protein and nutrient content.
Naturally sweetened – These muffins are sweetened naturally with maple syrup and fresh grated apples, then finished with a crunchy sugary crumb topping.
Fresh Apple Flavor: Grated apples keep the muffins moist and full of natural fruit flavor. charm.
Perfect Anytime Treat: Great for breakfast, snacks, or cozy fall mornings with a cup of coffee.

There’s something special about the smell of apple and cinnamon baking in the oven — it instantly makes your kitchen feel cozy and inviting. These Apple Cinnamon Muffins are made with wholesome einkorn flour, naturally sweetened with maple syrup, and packed with freshly grated apples. Each muffin is finished with a crunchy walnut cinnamon-sugar topping that turns an everyday muffin into a bakery-worthy treat.

Einkorn flour gives these muffins a tender crumb and a slightly nutty flavor that pairs beautifully with the warm spices and juicy apples. Because einkorn absorbs liquid differently than modern wheat, the grated apple helps keep the muffins moist without needing a lot of added fat or sugar. It’s a small tweak that makes a big difference in both texture and nutrition.

These muffins are wonderful fresh out of the oven, but they also keep well for a few days — perfect for busy mornings, school snacks, or a wholesome afternoon pick-me-up. Whether you’re new to baking with einkorn or it’s already a pantry staple, this is one of those easy, cozy recipes you’ll find yourself coming back to again and again.

Ingredients needed for these einkorn apple muffins

For the muffins

Melted butter
Maple syrup
Eggs
Shredded apples
Vanilla extract
Einkorn flour
Fine grain sea salt
Cinnamon
Cardamon
Baking soda
Baking powder

For the topping

Chopped walnuts
Melted butter
Einkorn flour
Coconut sugar
Maple sugar or Granulated sugar
Cinnamon

Tips

Lightly squeeze excess juice (only if very wet).
If your grated apples are extremely juicy, gently press out some liquid. Too much moisture can make the muffins gummy, especially with einkorn’s softer gluten.

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Step By Step Directions-How to make einkorn apple cinnamon muffins

Prep ingredients

In a medium bowl, whisk together einkorn flour, baking powder, cinnamon, cardamom, baking soda, and fine sea salt. Set aside. In a large bowl combine wet ingredients, cooled melted butter, maple syrup, eggs, vanilla extract.

Whisk and fold in apples

Whisk together your wet ingredients until well combined. Then fold in apples.

Add flour

Add flour mixture and mix until just combined.

Make topping

Let the muffin batter rest while you make the crumb topping. To a bowl combine crumb topping ingredients and mix until course sand/crumbles form.

Fill muffin tins & bake

Line a 12-cup muffin pan with paper liners, then evenly divide the batter among the cups. Sprinkle the crumble topping over each muffin and bake for 16–20 minutes, until the tops are golden and a toothpick inserted in the center comes out clean or with a few crumbs.

Pro Tip

For a crunchier topping texture that lasts, replace either the coconut sugar or the maple sugar with granulated sugar—this helps the topping stay crunchy for longer.

Frequently Asked Questions

Where to buy einkorn flour?

With einkorn flour gaining popularity it has become much easier to source it locally at more grocery and specialty stores. I like the consistency of jovial einkorn flour. It typically weighs close to 120 grams per cup which makes it easy for beginners just getting started, especially if you aren’t actively using a scale to measure your flour.

I also, am a huge fan of farm2flour brand as it is freshly milled, within 7 days of being shipped to your house, it smells and tastes amazing, and I find it to be a better bang for your buck especially because you can subscribe or buy in bulk to avoid shipping costs. The more you buy, the better the price per pound. For instance, a 5lb bag of their einkorn is $3.40 per pound, compared to $5.12 per pound for the 2lb bag. I’ve found that ordering 30lbs at a time offers the best deal with free shipping on anything over $99.

Cooking with Einkorn flour is usually pretty straightforward, often being a 1:1 or sometimes a 1:1.25 replacement for regular all-purpose flour in most recipes, but there are some notable differences to keep in mind if your recipe isn’t producing the quality product you’d like. Einkorn flour is more dense than regular flour due to its low gluten content, it absorbs less fat and liquids than modern wheat flours and at a much slower absorption rate. The adjustment of liquid may be necessary in some recipes, especially those that require refrigeration.

Can I use apple sauce in replace of shredded apples?

Yes, you can substitute applesauce for the shredded apples—use about ½ cup of applesauce in place of the shredded apple. However, fresh shredded apples provide a stronger, more vibrant apple flavor and are highly recommended for the best results in this recipe.

What type of apples should I use?

I recommend a sweet apple like honeycrisp, gala or fuji. Avoid tart apples, such as granny smith.

How to keep the crumble topping crunchy?

This recipe uses both coconut sugar and maple sugar in the crumble topping to keep it refined sugar–free and naturally sweetened. These sugars give a rich, caramel-like flavor, but they tend to soften at room temperature.

If you prefer a crunchier topping that holds up longer, replace either the coconut sugar or the maple sugar with granulated sugar. Granulated sugar caramelizes and hardens slightly as it bakes, creating a crisp texture that lasts. For best results, allow the muffins to cool completely before storing, and keep them loosely covered—too much trapped moisture can soften the topping.

Coconut sugar and maple sugar naturally contain more moisture and have a lower melting point than granulated sugar. While they add depth of flavor, they absorb humidity from the air over time, which is why the crumble topping made entirely with them will soften more quickly.