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Healthy Lemon Poppy Seed Muffins

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A healthier take on a classic flavor, these Whole Grain Lemon Poppy Seed Muffins are made using whole grain flours, a little oil and happen to be dairy-free. Moist, flavorful and perfect for lemon lovers!

glazed lemon poppy seed muffin this recipe

Recipe and post originally published in March 2016. Photos and recipe slightly updated (with better results!) March 2020.

Is anyone else obsessed with lemon poppy seed? It’s one of my FAVORITE flavors and Lemon Poppy Seed Muffins are one of my top favorite muffins.

Basically if I am picking baked goods it’s:

  1. chocolate (and/or peanut butter)
  2. banana (and/or peanut butter)
  3. lemon

Not necessarily in that order… it definitely depends on the baked good or dessert.

A Healthy Lemon Poppy Seed Muffin Recipe

These lemon poppy seed muffins use a mix of whole wheat white flour and oat flour. I like using oats here for a little fiber boost but between you and me… I’ve made this recipe with just whole wheat pastry flour and the results are just about the same.

However you decide to make these muffins, they’re moist and bursting with lemon-y goodness.

AND They’re made with some healthier ingredients including >>

  • whole wheat white flour
  • oat flour
  • freshly squeezed lemon juice
  • a non-dairy milk of choice
  • coconut oil
half lemon muffins on pink plate

Let’s Talk About How Lemon Muffins

Muffins are easy peasy, lemon squeezy. You can use an electric mixer to speed things up, or mix by hand.

Get out all of your ingredients, bowls, measuring cups and muffin pan and let’s get to it.

Step 1 – lemon juice + milk

We’re essentially making a homemade buttermilk here by adding the lemon juice and milk together. I like to use my glass measuring cups for this.

Step 2 – mix dry ingredients

Add the flours, poppy seeds, baking powder, baking soda, salt and lemon zest in one bowl and set aside.

Step 3 – mix wet ingredients

Whisk together the sugar with oil, then add in eggs and the milk-lemon mixture.

Step 4 – time to combine

Now it’s time to combine the ingredients together to create the lemon poppy seed muffin batter.

mixing bowl with lemon poppy seed muffin batter

Step 5 – transfer to muffin pan

You can spray with oil, use liners, or use a silicone pan.

Evenly distribute muffin batter into the 12-cup muffin pan, filling about 3/4 way full.

lemon poppy seed muffin batter in muffin pan
Top with even more lemon zest if you’d like!

Step 6 – Now we Bake

Bake the muffins at 375ºF for about 15 minutes – check with inserted toothpick at this time for wet batter. If just little crumbs (or no crumbs) comes out on toothpick, your muffins are done!

cooled lemon poppy seed muffin in pan

And a little lemon glaze is always a good idea with muffins. You can mix about 1/2 cup powdered sugar with 1/2 tsp lemon juice for a drizzle glaze.

You could also opt for melted coconut butter!

Or leave plain…

half of lemon poppy seed muffin with glaze

Whatever you decide, these muffins need to get on your list!

If you make this recipe, be sure to leave a comment and review below! I love hearing from you, and it helps others learn about the recipe too! Xx Ashley

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Healthy Lemon Poppy Seed Muffins

glazed lemon poppy seed muffin
Print Recipe

★★★★★

5 from 4 reviews

A healthier take on a classic flavor, these Whole Grain Lemon Poppy Seed Muffins are made using whole grain flours and coconut oil. Dairy free!

  • Author: Ashley
  • Prep Time: 10 mins
  • Cook Time: 15 mins
  • Total Time: 25 mins
  • Yield: 12 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American
  • Diet: Vegetarian

Ingredients

Scale
  • 1 cup whole wheat white flour (or whole wheat pastry)
  • 3/4 cup oat flour
  • 2/3 cup granulated sugar 
  • 2.5 tablespoons poppy seeds
  • 2 teaspoons baking powder
  • 1/4 teaspoon baking soda
  • 1/2 teaspoon fine sea salt
  • zest of 3 medium lemons
  • 1/4 cup room temperature non-dairy milk (oat, cashew, coconut, etc.)
  • 1/3 cup of freshly squeezed lemon juice, approximately 3 small lemons
  • 2 large eggs, room temperature
  • 1/3 cup coconut oil, melted & cooled (or avocado)
  • 1/4 teaspoon pure almond extract (or vanilla)

Instructions

  1. Preheat oven to 375ºF and line muffin pan with liners or grease with oil; set aside.
  2. In a glass measuring cup add lemon juice and milk together, set aside.
  3. In a medium bowl stir together both of the flours, poppy seeds, baking powder, baking soda, salt and lemon zest. Set aside.
  4. In a large bowl whisk together oil, sugar and egg; slowly stir in lemon-milk until combined.
  5. Add dry ingredients to bowl of wet ingredients, slowly stirring until just combined (don’t overmix).
  6. Evenly disperse batter into greased muffin pan, filling about 3/4 way full. 
  7. Bake muffins for 15-20 minutes, checking muffins at 15 minutes with inserted toothpick. Allow muffins to cool in pan for 5 minutes before transferring to wire rack. 
  8. Store muffins in container at room temperature – best enjoyed within 3-4 days.

Notes

FLOUR: You can also use unbleached all-purpose flour. I would add 2 more tablespoons if going this route.

*When using melted coconut oil, it is always a good idea to use the rest of the ingredients at room temperature, as to make sure the coconut oil does not solidify. Just set out your egg and milk about 30 minutes before prepping the rest of the ingredients.

Nutrition

  • Serving Size: 1
  • Calories: 204
  • Sugar: 12
  • Sodium: 238
  • Fat: 6
  • Saturated Fat: 4
  • Unsaturated Fat: 2
  • Trans Fat: 0
  • Carbohydrates: 32
  • Fiber: 1
  • Protein: 3
  • Cholesterol: 16mg

Keywords: Lemon Poppy Seed Muffins, healthy muffins

Photos by: Erin Alvarez.

About Ashley

"Ashley Walterhouse is the founder of Fit Mitten Kitchen, based in the Greater Lansing Area of Michigan, AKA “the Mitten.” Ashley grew up as a picky eater but later discovered that eating healthy was actually easy and fun. She started FMK in 2015 as a way to share her newfound love of developing healthier recipes for all to enjoy."

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  2. Emily says

    Isn’t it awesome that God created the world with SO many different types of foods that we can pair with each other to make things like LEMON POPPY seed muffins? :))) Lemon poppy seed is one of my favorite light, spring time flavors. 🙂

    Reply

  5. Chrissa - Physical Kitchness says

    I’d say your ability to make amazing treats trumps your crappy zesting abilities! These look AMAZEBALLS! I love love love baked goods with lemon flavors. So light and perfect for breakfasts. Dang girl, you nailed it again!

    Reply

  8. Kaitlin says

    I bet that lemon flavor is divine! I always find that no matter the way in which I zest, most of it ends up on the zester and not my bowl!

    Reply

    • Ashley says

      I am going to have to get myself a microplane STAT, then come back and share another recipe and compare 😉 Thanks Kaitlin!

      Reply