The Ultimate Healthy Lemon Poppy Seed Muffins {Recipe Video!} | Amy's Healthy Baking (2024)

An easy & skinny recipe for classic lemon poppy seed muffins! They taste just like the ones from a bakery but have NONE of the guilt!


Throughout my childhood, my parents planned multiple family vacations to Disneyland. Since we usually drove eight hours down I-5 to visit my grandparents in San Diego instead of flying (if you’ve ever driven on that freeway in California, you know how monotonous the trip through miles and miles of plain yellow fields can be!) and Anaheim was on the way, it was easy to hop off of the highway and stop at The Happiest Place on Earth for a few days first.

We always stayed at the same hotel, situated just two stoplights away from the freeway and one block from the Disneyland entrance. That made life really easy for my parents… The short little legs of young kids can only walk so fast (and so far before they start complaining!).


As really early risers—my brother and I regularly woke up by 6 am every day—we walked over to the park before most of the crowds arrived and usually were the first in line when the gates opened at 8 am. We spent all morning dashing between the most popular “kiddie” rides, like Dumbo and Peter Pan and the Teacups, before the lines grew too long for our patience.

Then our very smart parents walked us back to the hotel shortly after lunch for a bit of quiet time before we could get tired or cranky (they preferred us taking naps, but my brother and I often refused and silently read books instead!) and swimming in the pool. Sometimes we went back to Disneyland for a couple of hours to squeeze in a few more rides or some souvenir shopping, but other times we just collapsed into bed from exhaustion!


Because theme park food costs an arm and a leg, our parents always packed our own. They filled a backpack with water bottles, apples, fruit snacks, crackers, and a jar of peanut butter for whenever a “rumbly in our tumblies” hit (we loved Pooh Bear!), and we ate PB&J or ham and cheese sandwiches in the hotel room for dinner.

Yet out of all of those meals, I loved breakfast the most. At home, we always poured a bowl of cereal with milk, but since the hotel room lacked a fridge, Mom bought a package of jumbo-sized muffins from the local grocery store bakery as a special treat instead.


As picky eaters, my brother and I only ate one flavor: lemon poppy seed. (We would’ve gladly gone with double chocolate, but Mom drew the “special treat” line there!) And the lemon poppy seed muffins had to be plain… So we always picked off all of the slivered almonds if those were the only ones Mom could find!

Since we were so small, Mom gave us each half of a jumbo muffin morning for breakfast, and I loved every single bite. The sweet lemon flavor… The tiny little barely crunchy seeds… Those moist, tender crumbs… I easily would’ve polished off the second half if she let me. I definitely didn’t care about calories or healthy food back then!


But times have changed, and even though I still love Disneyland just as much, now I want my muffins to be a little healthier than the ones sold from grocery store bakeries. That’s exactly why I created this recipe for the Ultimate Healthy Lemon Poppy Seed Muffins! They’re supremely tender and full of that same sunshiny flavor, but they’re made from entirely wholesome ingredients and contain none of the guilt!


This easy recipe begins with white whole wheat flour. White whole wheat flour comes from finely grinding a special type of white wheat, whereas regular whole wheat flour is made from a heartier variety of red wheat. This gives white whole wheat flour a lighter taste and texture, almost like that of all-purpose flour, but it still has the same health benefits of regular whole wheat flour.

Note: Whole wheat pastry flour would be the perfect substitute! I’ve also included my favorite gluten-free flour blend in the Notes section beneath the Instructions, if you prefer.


Many traditional recipes include anywhere from ½ cup to 1 full cup of oil or butter—yikes!! Instead, this lighter version uses just 1 tablespoon of butter, and the rest of the tender texture comes from my favorite ingredient in healthier baking… Greek yogurt! Greek yogurt provides the same moisture as extra butter or oil for a fraction of the calories, and it gives your baked goods a protein boost, too!

To keep these muffins clean eating friendly, you’ll skip the granulated sugar and sweeten them with a combination of honey and vanilla crème stevia. Vanilla crème stevia is one of my new favorite finds! It’s a plant-based, no-calorie sweetener that’s clean eating friendly, and it’s very concentrated. A little goes a long way! I usually buy SweetLeaf, which is sold in a small bottle with an eyedropper, and you can find it at many health-oriented grocery stores, as well as online. (And you’ll use it in all of these recipes of mine, too!)


The bright citrus flavor comes from two sources: freshly squeezed lemon juice and lemon zest. The latter actually provides the majority of the sunshiny taste, so don’t skip it! I tested this recipe with varying amounts of zest, and all of my taste testers agreed that a full 2 ½ tablespoons had the best flavor.

The baking instructions are slightly different than your stereotypical muffin recipe. To make the muffins as tall and tender as possible, you’ll bake them starting at 425°F for 7 minutes. Then, without opening the oven door, reduce the temperature to 350°F for the rest of their baking time.

This brief stint at that really high temperature quickly activates the baking powder and baking soda. Along with an internal burst of steam, this makes the muffin tops rise really fast and stay nice and tall. Yes, it has to be 425°F—just turn your oven into a sauna, and your muffins will be happy!


And once they’ve cooled, so will your belly! ? And when you make your own, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! ?) I’d love to see your muffins and feature them in my Sunday Spotlight series!

The Ultimate Healthy Lemon Poppy Seed Muffins

3.9 from 15 reviews

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Yields: 12 muffins

These muffins taste like they’ve come straight from a bakery! They’re supremely tender and full of bright, sunshiny lemon flavor. The muffins will stay fresh for at least 5 days if stored in an airtight container in the refrigerator.

  • 2 ½ cups (300g) white whole wheat flour or gluten-free* flour (measured like this)
  • 1 tsp baking powder
  • ½ tsp baking soda
  • ¼ tsp salt
  • 1 ½ tbsp (13g) poppy seeds
  • 2 ½ tbsp (16g) lemon zest, freshly grated (about 3 large lemons)
  • 1 tbsp (15g) unsalted butter or coconut oil, melted and cooled slightly
  • 2 large egg whites, room temperature
  • 2 tsp vanilla extract
  • ½ cup (120g) plain nonfat Greek yogurt
  • 2 tbsp (30mL) honey
  • 1 ¼ tsp vanilla crème stevia
  • 6 tbsp (90mL) freshly squeezed lemon juice (about 2 large lemons)
  • ¾ cup (180mL) nonfat milk
  1. Preheat the oven to 425°F, and lightly coat 12 muffin cups with nonstick cooking spray.
  2. In a medium bowl, whisk together the flour, baking powder, baking soda, salt, poppy seeds, and lemon zest. In a separate bowl, whisk together the butter, egg whites, and vanilla. Stir in the Greek yogurt, mixing until no large lumps remain. Mix in the honey and stevia until fully incorporated. Mix in the lemon juice. Alternate between adding the flour mixture and milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 4 equal parts.)
  3. Divide the batter between the prepared muffin cups. Bake at 425°F for 7 minutes. Without opening the oven door, reduce the oven temperature to 350°F, and continue baking for an additional 12-15 minutes, or until the tops feel firm to the touch and a toothpick inserted into the center comes out clean. Cool in the muffin cups for 10 minutes before carefully transferring to a wire rack.

Notes: For the gluten-free flour, I recommend the following: 1 ¼ cups (150g) millet flour, ½ cup (60g) brown rice flour, ¾ cup (90g) tapioca flour, and 2 teaspoons xanthan gum. Most store-bought blends will work as well, if measured like this.

Whole wheat pastry flour, regular whole wheat flour, or all-purpose flour may be substituted for the white whole wheat flour.

Agave or pure maple syrup may be substituted for the honey.

Any milk may be substituted in place of the nonfat milk.

{gluten-free, clean eating, low fat, low calorie, low sugar}

View Nutrition Information + Weight Watchers Points

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The Ultimate Healthy Lemon Poppy Seed Muffins {Recipe Video!} | Amy's Healthy Baking (2024)

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