Moist Lemon Poppy Seed Muffins (Gluten-Free & Dairy-Free)

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You can now find the updated and fully formatted version of this recipe on my new site, Gluten-Free Heritage, where I’m sharing all my favorite + new recipes made with fresh-milled, gluten-free grains. 👉 Click here to view the full recipe: Fresh-Milled Lemon Poppy Seed Muffins (GF, DF) – Gluten Free Heritage

A fresh twist on a classic, made tender and allergy-friendly

I’ve been experimenting with lemon poppy seed muffin recipes lately, and while I loved the bright flavor of my first batch, the texture needed a little work. Millet flour can bake up dry if it’s not paired with the right supporting ingredients. So, I went back to the mixing bowl, inspired by a friend’s blueberry muffin recipe that had turned out incredibly moist and soft, and I set out to apply what I had learned.

By adjusting the muffin batter — swapping some of the flour, adding applesauce, and using just the right amount of healthy fat (hello, avocado oil!) — I found a winning combination. These muffins are now bright, tender, and completely dairy-free, boasting a fluffy texture that allows the fresh lemon flavor to shine through.

And the best part? They’re made with fresh eggs from my very own chickens and fresh-milled flour using my NutriMill Classic — adding even more love and nutrition to each batch. If you’ve been wanting to try milling at home, you can use this link and code VINTAGEVIRTUES for $20 off your own NutriMill.

Gluten-Free Lemon Poppy Seed Muffins (Made with Fresh-Milled Flour)

Yields: 12 muffins
Perfect for a quick breakfast or an afternoon snack.

Ingredients

Dry Ingredients (Large Mixing Bowl):

¾ cup fresh-milled millet flour
¼ cup fresh-milled oat flour
½ cup almond flour
¼ cup tapioca starch
2 tsp baking powder
¼ tsp baking soda
¼ tsp sea salt
1 tbsp poppy seeds

Wet Ingredients (Large Mixing Bowl):

½ cup maple syrup
¼ cup unsweetened almond milk (or other dairy-free milk like oat milk or refrigerated coconut milk, not canned)
¼ cup unsweetened applesauce
⅓ cup avocado oil (vegan butter or coconut oil)
Zest of 1 fresh lemon + 2 tbsp lemon juice
1 tsp vanilla extract (or try ½ tsp lemon extract for stronger citrus notes)
2 large eggs, farm fresh!

Most of these ingredients were purchased through Azure Standard or Thrive Market. You can get 40% off your first Thrive Market order here.

Instructions

Preheat oven to 350°F (175°C). Line a muffin pan with paper liners or lightly grease it.
In a large mixing bowl, whisk together all dry ingredients.
In a medium bowl or small bowl, whisk the wet ingredients until smooth.
Pour the wet mixture into the dry and stir just until combined. Let the batter rest for 5 minutes to allow the flours to hydrate.
Divide the batter evenly into the muffin cups, filling each about ¾ full.
Bake for 18–20 minutes, or until a toothpick inserted in the center comes out clean or with a few moist crumbs.
Cool muffins in the pan for 5 minutes, then transfer to a cooling rack to finish cooling completely.

Storage Tips

Store muffins in an airtight container:

At room temperature for 1–2 days
In the fridge for up to 5 days
Or freeze in a freezer bag for longer storage — they thaw beautifully for a quick, lemony sweet treat.

Why This Version Works

Millet and oat flour give structure and softness without gluten
Almond flour adds richness and moisture
Applesauce keeps the crumb tender without dairy or melted butter
Avocado oil provides a neutral, healthy fat
Farm-fresh eggs give the best texture and flavor
And the bright citrus flavor of fresh lemon zest and juice makes each bite pop!

Watch & Bake Along

Watch this quick video — it walks you through the full recipe in just 2 minutes!

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