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These lightly sweetened Gluten-Free Poppy Seed Muffins are creamy and bursting with citrus flavor. The recipe uses both lemon and orange zest for a double punch of citrus, with gluten-free rolled oats, and Greek yogurt for a bit of added protein.

Healthy lemon orange muffins are great for whipping up in the morning for breakfast, or meal prepping for the week. They are full of flavor from a combination of lemon zest, orange zest, lemon juice, and orange extract.
Each muffin contains only 141 calories and 5 grams of protein. They use coconut sugar, which has a lower glycemic index than regular sugar. This helps reduce insulin resistance and improve the ability to lose weight.
If you like citrus muffin recipes, you will love Raspberry Lemon Quinoa Muffins and Healthy Lemon Loaf!
Why You’ll Love This Recipe
- Duel Citrus Flavor: While many muffin recipes use lemon, these muffins use both lemon zest and orange zest, along with orange extract for double the citrus flavor.
- No Specialty Flour Required: Unlike many other gluten-free recipes, these healthy poppy seed muffins don’t use hard-to-find gluten-free flours. All you need are gluten-free rolled oats which blend into the batter.
- Quick and Easy Muffins: Using a food processor to blend the batter cuts down on mixing time, and they bake in just 20 minutes. That makes them great for a last-minute breakfast or for meal prepping.
- Low-Calorie Muffins: These poppy seed muffins have just 141 calories for a calorie conscious snack.
Table of Contents
Ingredients

- Greek Yogurt: Adding Greek yogurt to baked goods boosts the protein in the muffins and adds creaminess and tang.
- Eggs: Not only are eggs an excellent binder for baked goods, but they also contain a lot of low-calorie protein.
- Gluten-Free Rolled Oats: Be sure to use oats that are marked certified gluten-free and aren’t quick oats, so they don’t cook too quickly. Not gluten-free? Use regular rolled oats or oat flour!
- Lemon Juice and Zest: The juice of a lemon adds tartness and acidity to the muffins, while the zest adds more aromatic flavor.
- Orange Extract and Zest: Instead of adding more liquid with orange juice, use orange extract for a more concentrated flavor. The zest also adds the aromatic flavor of orange.
- Coconut Sugar: This sugar substitute has a lower glycemic index than regular sugar. If you want a zero-calorie option, you can use monk fruit instead.
- Poppy Seeds: These seeds have a slightly nutty flavor and add a pleasant crunch. Their flavor contrasts nicely with citrus.
See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.
Variations & Dietary Modifications
- Make Them Dairy-Free: You can make these muffins dairy-free by using a dairy-free Greek yogurt. It’s a simple substitute that tastes nearly the same.
- Add Berries: Citrus pairs well with berries such as blueberries, raspberries, blackberries, and strawberries. You can add any of them to these muffins for extra sweetness.
- Make Mini Muffins: Use a smaller muffin tin and cut the baking time in half to make bite-sized mini muffins. They are the perfect little mid-day snack or after-dinner dessert.
How to Make Gluten-Free Poppy Seed Muffins
These gluten-free lemon orange muffins are bursting with flavor without a lot of extra calories. All you need to make them is a food processor, a greased muffin pan with muffin liners, and an oven preheated to 375°F.

- Step 1: Blend the Ingredients. Add the oats, Greek yogurt, eggs, milk, orange extract, and lemon juice to a food processor. Blend the mixture on high for a few minutes until it’s smooth and creamy.

- Step 2: Add and Finish Blending. Add the coconut sugar, poppy seeds, lemon and orange zest, olive oil, baking powder, baking soda, and salt. Blend again until smooth and well incorporated.

- Step 3: Divide Mixture Into a Muffin Tin. Divide the batter evenly among the 12 muffin cavities. Bake them for 20 minutes until they are slightly golden. Remove them from the muffin tin and let them cool.

- Step 4: Top with Icing. While the muffins cook, whisk together the sugar and lemon juice to make a citrus icing. Drizzle it over the cooled muffins. You can skip the icing if you don’t want the extra sugar.
Expert Tips
- Use Room Temperature Ingredients: Use room temperature eggs, Greek yogurt, and almond milk to ensure the batter blends smoothly. A smooth batter results in light and fluffy baked goods.
- Don’t Skip the Zest: Citrus zest has a more concentrated aromatic flavor. It’s perfect for baked goods because it adds a punch of citrus without adding excess liquid.
- Be Careful Not to Overmix: Only mix the batter until it is smooth, and the ingredients are just combined. If you mix the batter too much, then the muffins will turn out dense and gummy instead of fluffy.
- Storing: Keep leftover citrus muffins in an airtight container in the refrigerator for up to 5 days. You can also freeze them for up to 3 months.

Serving Suggestions
These low-calorie poppy seed muffins are the perfect citrus-forward muffin. They are light in both texture and flavor, which is great for spring or summer. However, the lower calorie content and slightly higher protein make them great for eating all year round for breakfast or a snack.
- If you want to enjoy these muffins for breakfast, you should pair them with more protein. Try my healthy breakfast quesadillas for an easy and delicious meal.
- Fuel your afternoon with these gluten-free poppy seed muffins and a high fiber protein smoothie.
- The citrus flavor of these muffins makes for a great dessert to enjoy after a citrus-forward meal like lemon chicken zucchini noodles.

Gluten-Free Poppy Seed Muffins Recipe FAQs
No, while oats are naturally gluten-free, they are often processed in the same locations as wheat so there is the possibility of cross-contamination. If you must eat gluten-free, be sure to look for oats that are labeled gluten-free. If you don’t need your muffins to be gluten-free, you can use regular rolled oats or oat flour instead.
There are a variety of reasons why your muffins didn’t rise. It may have been because the ingredients were too cold, you didn’t use the correct amount of leavening, or it wasn’t fresh. To ensure this doesn’t happen, remove any chilled ingredients from the refrigerator 30 minutes before mixing, make sure you measure all your ingredients properly, and that your leavening is fresh.
Sure! If you have concerns about baking with poppy seeds, you can use chia seeds instead. They have a similar flavor and texture.
More Delicious Gluten-Free Muffin Recipes
If you tried this Gluten-Free Poppy Seed Muffins recipe or any other recipe on my website, please leave a 🌟 star rating and let me know how you go in the 📝 comments below.
















The lemon poppyseed muffins look amazing. Please would you tell me how to make the topping?! Yummy
What topping? There isn’t a topping for the muffins.
I make breakfast for dinner one evening each week…this is on tonight’s menu with some scrambled eggs and sausage…they sound divine! What brand of flour do you use, though?
This one -> Gluten Free 1 to 1 baking flour
These look heavenly! I am drooling over here!!!
Thanks girl! 🙂
yum, these look so good!! I actually really enjoy cleaning… when I don’t HAVE to do it. I usually clean to avoid something else I don’t want to do. 🙂
I so do the whole clean to avoid doing real work too! I think it helps me destress.
Pinned this one, for sure! I can’t wait to try these, especially since I have a thing for lemon and poppy seed! Thanks!
–G
http://gingerwroot.com
You will love for sure!
I was so proud of myself for baking this weekend! The sunshine totally put me in a good mood. And YEAH teaching kids swimming lessons will totally wear you out! How are you even still moving!
Hence why I go to bed when I get home! What did you make me?
I’m such a sucker for lemon poppyseed anything. YUM.
I second Blair– you must be very patient to be teaching swim lessons. I did swim team growing up and we did everything in our power to not listen and just goof off in the pool (“I can’t hear there’s water in my ears”).
In all seriousness, I think those moments when it feels “meant to be” are so important because it means you’re right where you’re supposed to be 🙂 I’m so happy for you!
This seriously happened in tonight’s class. None of the kids wanted to do anything I asked and they all complained about water in their ears. AGHGHGH…some days you can’t win!
These sound awesome! So much citrus!
And bless you for teaching swimming lessons…I can hardly handle my own children in the pool!
That just made me laugh. I didn’t feel much like a saint tonight with all the yelling I had to do at the kids. They’re a handful.
I love the addition of greek yogurt in baked goods, it makes them so fluffy! These muffins look so good, can’t believe they are only 123 calories each!
It’s one of my favorite ingredients and keeps the calorie count low!
As soon as we run out of muffins or cookies I have to bake too. These look so fluffy and delicious!
Thank you! Hope you had a good race today.