Healthy lemon poppy seed muffins made with oat flour, dairy-free Greek yogurt, and sweetened only with maple syrup. They’re light and fluffy and taste extra indulgent with an optional lemon glaze. 

Healthy lemon poppy seed muffins with glaze

Nothing says spring like lemon desserts! A few of my favorites that come to mind include lemon bars, lemon cookies, and of course, lemon poppy seed muffins. I love lemon poppy seed muffins, especially my mom. Her lemon poppy seed muffins always made an appearance at Easter brunch and were a highly requested dessert at any spring or summer party. Basically, my mom was known for her muffins.

To carry on this tradition. I’m bringing you these healthy lemon poppy seed muffins. They’re light, fluffy, and bursting with an intense lemon flavor. If you love lemon dessert, promise me you’ll give these muffins a try!

Healthy Lemon Poppy Seed Muffins

These lemon poppy seed muffins are a healthier muffin made with oat flour, dairy-free Greek yogurt, and only sweetened with maple syrup. I love baking with oat flour since it’s a whole grain, naturally gluten-free and can easily be made from rolled oats in a high-speed blender.

Using dairy-free yogurt like Kite Hill almond milk yogurt makes these muffins tender and moist. The almond milk yogurt is comparable to 2% or whole milk Greek yogurt, so if you can tolerate dairy, feel free to substitute organic regular Greek yogurt in its place.

The maple syrup balances out the tart lemon juice while keeping them naturally refined sugar-free. Feel free to swap out the maple syrup for honey if that’s what you have on hand. To add an extra layer of sweetest and make the muffins a little more dessert-like, they have a simple lemon glaze made from powder sugar and lemon juice. This is 100% optional. but does make the muffins extra delicious.

close up Healthy lemon poppy seed muffins with glaze 
Healthy lemon poppy seed muffins with glaze
close up Healthy lemon poppy seed muffins with glaze

Nourished by Nutrition Facts

Oat Flour

This whole-grain flour is my go-to for healthier gluten-free baked goods. Since oat flour is just blended up rolled oats, it has all the nutrition benefits of oatmeal, inlcuding the vitamins, minerals, antioxidants, and fiber! One ½ cup serving of oats provides 4g of fiber and contains both soluble and insoluble. Oats are an excellent source of soluble fiber called beta-glucans. Soluble fiber draws water into your intestinal tract. This type of fiber helps support regular digestion, helps us feel fuller, and can help lower cholesterol and blood sugar levels. (1)

While you can’t technically substitute all-purpose or whole wheat flour 1:1 with oat flour, I find with a little tweaking to the recipe, you still get a delicious baked good. If you need gluten-free recipes or like to keep the amount of gluten you consume to a minimum, baking with oat flour is a great option.

Poppy Seeds

As the name indicates, poppy seeds are the seeds from the poppy plant, Papaver somniferum. Poppy flowers are known for producing opium, which is used in manufacturing drugs like morphine and codeine. But don’t let that deter you from consuming poppy seeds! The seeds shouldn’t contain opium. The opium comes from poppy latex, a substance found in the poppy pod.

Poppy seeds pack a nutritional punch for being so small. Poppy seeds are a good source of calcium, manganese, magnesium, phosphorus, and iron. For instance, one teaspoon of poppy seeds contains 4% of your daily calcium. (2) An easy way to incorporate poppy seeds is to add them to smoothies, baked goods or salad dressings.

Healthy lemon poppy seed muffins with glaze

inside of Healthy lemon poppy seed muffins with glaze

IF YOU LOVE THese Lemon Poppy Seed Muffins, YOU’LL ALSO ENJOY…


Healthy Lemon Poppy Seed Muffins

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Healthy lemon poppy seed muffins made with oat flour, dairy-free yogurt, and sweetened only with maple syrup. They’re light and fluffy and taste extra indulgent with an optional lemon glaze.

  • Prep Time: 15 min
  • Cook Time: 15 min
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x


Units Scale

2 cups oat flour

1 teaspoon baking powder

1/2 teaspoon baking soda

1/4 teaspoon salt

1 1/2 tablespoon poppy seeds

1 tableespoon lemon zest

2/3 cup plain dairy-free or regular yogurt*

2 eggs

1/3 cup maple syrup

1/4 cup lemon juice

3 tablespoons avocado or melted coconut oil


Preheat the oven to 350F. Prepare a muffin tin by coating lightly with avocado or coconut oil or using muffin liners.

In a large bowl, combine the oat flour, baking powder, baking soda, and salt. Mix to combine. Next, add in the lemon zest and poppy seeds and mix again to evenly distribute throughout the flour mixture.
In a separate bowl, whisk together the yogurt, eggs, maple syrup, lemon juice, and oil. Add the mixture to the dry ingredients and mix until just combined.

Evenly distribute the batter into the prepared muffin tin, filling the cups about 3/4 of the way. Place in the oven and bake for 15-17 minutes. The muffins are done when a toothpick comes out clean.
Let cool for 5 minutes in the muffin tin then move to a wire cooling rack to cool completely. Once the muffins are cool, drizzle with the lemon glaze.

To make the glaze, add 1/2 cup powdered sugar to a bowl and mix in 1 tablespoon of lemon juice. If the glaze is too thick, add more lemon juice 1/2 teaspoon at a time until you reached the desired consistency. Likewise, if the glaze is too thin, add more powdered sugar 1 tablespoon at a time.

Store in an airtight container on the counter for 3 days or in the fridge for 5 days. The muffins can also be frozen for up to 3 months.


* I originally used use Kite Hill Greek-style almond yogurt. However, I do not love the new formula. I now use Kite Hill regular almond milk yogurt. You can sub 2% Greek yogurt or coconut yogurt.

Vegan option: I have not tested these without eggs, but based on other recipes use flax eggs should work just fine. I recommend 2 tablespoons of ground flax + 5 tablespoons of warm water



I’d love to hear how it turned out for you! Leave a comment below and share a picture on Instagram with the hashtag #nourishedbynutriton.