Healthy Lemon Poppy Seed Muffins

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These light and brightly flavored Healthy Lemon Poppy Seed Muffins, which are also gluten free, are fantastic for on-the-go breakfasts or snacks. Easy to freeze!

These healthy lemon poppy seed muffins are perfect for springtime (hello, Easter brunch!), but equally delicious any time of the year. Tender with perfectly browned edges and filled with fresh lemon flavor.

Irresistibly good! In fact, my family seems to transform into a school of piranhas whenever I make any muffin recipe, whether it’s these lemon ones or other favorites, like Banana Blueberry Muffins or Carrot Muffins.

And that’s exactly why I also make a double batch. Eat one right away, freeze the other.

WHAT YOU NEED FOR THIS HEALTHY LEMON POPPY SEED MUFFINS:

These are the main ingredients needed for this recipe (affiliate links included)…

• OAT FLOUR: Oat flour can be purchased in many well-stocked grocery stores and health food stores. I like the Bob’s Red Mill brand. Double check that the brand is gluten-free if following a gluten-free diet. It is also easy to make oat flour at home from old-fashioned oats. See How to Make Oat Flour.
• POPPY SEEDS: Find poppy seeds in the spice section at the grocery store.
• LEMON: Use the zest and the fresh lemon juice. Give them lemon a good wash before grate the outside of the peel with a zester.
• APPLESAUCE: Use unsweetened applesauce.
• YOGURT: Use plain nonfat Greek yogurt.
• SUGAR: The recipe calls for coconut palm sugar, but brown sugar is a good substitution.
• EGG: One large egg.
• BAKING SODA: Make sure your baking soda is fresh!
• SALT: Use regular iodized salt.
• OIL: I like to use avocado oil, but any neutral oil works.

See recipe card below for full ingredients list & recipe directions.

?What’s to love about this poppyseed muffin recipe:

▪️Easy snacks: Keep these on hand for easy snacks or grab-and-go breakfast options. They’re fantastic with a cup of coffee or tea, and are endlessly kid-friendly. Make a double batch and freeze the extras.

▪️Healthier: Most of the oil is substituted with nonfat Greek yogurt and unsweetened applesauce. Plus, the muffins are made with whole wheat pastry flour, which adds an extra dose of fiber.

▪️Taste and texture: Tender with a fresh lemon flavor…everything you could ask for in a spring-inspired muffin!

How do you make poppy seed muffins?

This recipe follows the basic formula that I used for healthy muffins.

1. Start by mixing the dry ingredients in a bowl – in this case, that’s oat flour (more on that later), baking soda and salt. Stir in any extra spices or dry flavorings, such as poppy seeds and lemon zest. A whisk works best to combine it all evenly.
2. Stir together the wet ingredients in a large bowl – yogurt, applesauce, egg and lemon juice.
3. Pour the dry ingredients into the bowl with the wet ingredients and stir until just combined. Over-mixing makes for tough muffins. For tender muffins, take care to mix just until the flour is incorporated into the wet ingredients.
4. Scoop the batter into prepared muffin tins and bake! Use a large cookie scoop (like this one) or a 1/4-cup measure to scoop out even portions of the batter.
5. Let the muffins cool in the muffin pan for about 10 minutes before removing and cooling completely on a wire rack. An offset spatula works well to pop the muffins out of the tin.
6. Serve, store the muffins in an airtight container or freeze for later. More on freezing later!

Add a lemon glaze (optional):

To turn these muffins into a healthy-ish treat, make a quick glaze to drizzle over top. Stir together some powdered sugar, fresh lemon juice and a tablespoon or two of skim milk in a small bowl. Add enough milk to reach the desired consistency.

What are the benefits of oat flour?

• If you follow a gluten free diet, oat flour is a great option for baking. Be sure to use oat flour that is certified gluten free, such as this one. If making your own oat flour (more on that in a moment), use gluten free oats.
• Oat flour boasts a plethora of nutrients, including fiber, protein, phosphorous, magnesium, iron, potassium, zinc and others.
• Oats and oat flour have been shown in studies to lower cholesterol levels and reduce the risk of heart disease.
• How to make oat flour – Simply place the oats in a food processor and mix until it reaches a very fine consistency. To remove any leftover lumps, run the flour through a sifter. For more detailed instructions, see my post on How to Make Oat Flour.

Frequently Asked Questions:

How do you tell when muffins are done?

There are two ways to tell when muffins are done. First, press gently on the top of the muffin. When it’s done, it should feel firm, but with a bit of give. The muffin should spring back when pressed.
If the muffin feels firm to the touch, double check by inserting a toothpick or wooden skewer into the center of the muffin. If the toothpick comes out clean, the muffin is cooked through. If there is any batter on the toothpick, pop the muffins back into the oven for another minute or two.

Can you freeze poppy seed muffins?

Yes, poppy seed muffins freeze well. Allow the muffins cool to room temperature. Place them in a ziplock freezer bag in a single layer, squeeze out all of the air, then freeze. Alternatively, freeze the muffins in a large freezer-proof airtight container, like this one or this one.
The muffins can be frozen for up to 3 months when stored properly.

How long do lemon poppy seed muffins last?

When stored properly in an airtight container, the muffins should stay fresh for up to 3 days at room temperature or for up to 5 to 7 days in the refrigerator.

• 1 ½ cups oat flour be sure it’s certified gluten free (See Note)
• 1 teaspoon baking soda
• ½ teaspoon salt
• 1 tablespoons + 1 teaspoon poppy seeds
• grated zest of 2 lemons
• ¾ cup unsweetened applesauce
• ½ cup plain nonfat Greek yogurt
• ½ cup coconut palm sugar or brown sugar
• 2 tablespoons avocado oil or canola oil
• 1 egg
• 2 tablespoons fresh lemon juice

Cook ModePrevent your screen from going dark

• Preheat the oven to 375 degrees F. Lightly coat a muffin tin with cooking spray.
• In a medium bowl, whisk together the oat flour, baking soda and salt. Stir in the poppy seeds and lemon zest.
• In a large bowl, combine the applesauce, Greek yogurt, coconut palm sugar, canola oil, egg and lemon juice. Stir together until the mixture is smooth.
• Stir the dry ingredients into the applesauce mixture until combined. Do not overmix.
• Scoop the muffin batter into the prepared muffin tin.
• Bake until a toothpick inserted in the center of one of the muffins comes out clean, 12 to 14 minutes.
• Allow the muffins to cool in the tin for 5 minutes, then transfer to a rack and allow to cool completely. Serve or store in an airtight container.

Note: Oat flour can be purchased in many well-stocked grocery stores and health food stores. I like the Bob’s Red Mill brand. It is also easy to make oat flour at home from old-fashioned oats. See How to Make Oat Flour. Please note that I am not a medical or nutritional professional. I provide nutritional information for my recipes as a courtesy to my readers. It is calculated using the LoseIt! calculator and Weight Watchers points are calculated using the Recipe Builder on their site. While I attempt to provide information that is as accurate as possible, you should calculate the nutritional information independently before relying on it. Serving: 1Muffin | Calories: 127.7kcal | Carbohydrates: 18.4g | Protein: 4.3g | Fat: 4.3g | Saturated Fat: 0.5g | Cholesterol: 15.9mg | Sodium: 159.4mg | Fiber: 1.6g | Sugar: 8.3g If you make this recipe, I’d love to see it on Instagram! Just use the hashtag #COOKINCANUCK and I’ll be sure to find it.

This post was first published on February 19, 2018 and updated on March 3, 2022.

Disclosure: We are a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for us to earn fees by linking to Amazon.com and affiliated sites.
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