My brother’s birthday is coming up! Because he adores lemon treats—anything from cookies to cupcakes to scones to cheesecake and more—I’m helping him celebrate by declaring this Lemon Week on the blog. I don’t know who’s more excited about that… Me, who gets to bake everything, or him, who gets to eat it all!
Right before I finished elementary school, my family moved across town to an older yet larger house with huge front and backyards. Soon after we unpacked the most important boxes and stocked the fridge with fresh groceries, we all walked around outside, exploring the property with all of its hidden gems.
The first things we noticed were the trees—there were so many of them and countless different varieties! Not just your typical California redwoods either… We found orange, grapefruit, fig, bay leaf, apple, peach, plum, wild plum, avocado, and lemon trees scattered around the backyard grass and small hill behind the bedrooms.
Other than grabbing a fresh bay leaf every time Mom cooked spaghetti sauce, we picked fruit from the lemon trees the most. With three different trees to choose from—a Meyer lemon tree, one tree that bore lemons the size of footballs, and a third that lay dormant for at least 6 years after we moved in—we hardly ever ran out.
Since I was actually visiting my parents last week, I walked out into the backyard and plucked a few lemons from the tree just like I did throughout my childhood, and I used one of them for these Healthy Blueberry Lemon Poppy Seed Protein Muffins. When my brother arrived after spending the weekend at a friend’s, he was so surprised—and super happy to start his birthday celebrations a week early on such a sweet and healthy note!
To make these muffins both clean-eating friendly and low-carb, we’ll need two important ingredients: coconut flour and protein powder. Coconut flour behaves very differently than any other flour! It’s about 3 times as absorbent, so we’ll only use a little bit because adding too much will dry out the muffins.
For this reason, it’s extremely important to measure the coconut flour using either this method or a kitchen scale. I highly recommend the latter! I own this inexpensive kitchen scale, and it’s the #1 reason why my baked goods turn out with the perfect taste and texture every time I make them.
This recipe is designed for whey-based protein powder. I used Jamie Eason’s Lean Body for Her vanilla whey protein powder, and I loved how its whey taste was less noticeable than in some other brands. Unfortunately, it’s no longer sold in stores, but this protein powder (another one of my favorites!) and this protein powder are very similar.
Other brands of whey-based protein powder may work, but remember, many protein powders behave differently in baking recipes! Some are slightly more absorbent and will require a touch more milk; others are less so and may need a bit more coconut flour. See my Protein Powder FAQ Page for more information!
Note: I do not recommend using plant-based protein powder in this recipe. In general, plant-based protein powders are much more absorbent than whey-based protein powders, so the muffins would most likely turn out dry and crumbly.
To keep these muffins as light and healthy as possible, the batter only includes 1 tablespoon of coconut oil. Yes, that’s it! The rest of their tender, cupcake-like texture comes from my favorite ingredient in healthier baking: Greek yogurt. It adds the same moisture as extra butter or oil for a fraction of the calories, and it gives the muffins an extra protein boost too. That’s definitely a win-win!
The majority of the citrus flavor comes from the lemon zest. So pretty, pretty please, don’t skip it! I generally use Meyer lemons because the tree in my parents’ backyard bears so much fruit, but regardless of the variety you select, try to pick lemons without any green splotches on the skin. The more yellow its color, the brighter the lemon flavor will be!
When it comes to muffins, I generally prefer fresh blueberries because they don’t bleed as much and won’t turn the batter a grayish color like frozen. Either will work though! If you prefer frozen blueberries, set aside a tablespoon of the coconut flour/protein powder mixture, and simply toss the frozen berries with that before gently folding them into the batter to minimize any discoloration.
Now aren’t those muffins gorgeous?? Apparently my family thought so too because the entire batch disappeared in a heartbeat… Guess I need to bake more for my brother’s birthday brunch this weekend! 😉
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 healthy blueberry lemon poppy seed protein muffins!

Healthy Blueberry Lemon Poppy Seed Protein Muffins
Ingredients
- ½ cup + 2 tbsp (56g) coconut flour (measured like this)
- 2 scoops (84g) vanilla whey protein powder (really important – read Notes before beginning!)
- 1 tsp xanthan gum
- ¾ tsp baking powder
- ¾ tsp baking soda
- ¼ tsp salt
- 1 tbsp (8g) poppy seeds
- 1 tbsp (5g) lemon zest (about one medium)
- 1 tbsp (14g) coconut oil or unsalted butter, melted and cooled slightly
- 1 large egg, room temperature room temperature
- 1 tsp vanilla extract
- ¼ cup (60g) plain nonfat Greek yogurt
- ¼ cup (60mL) agave
- 3 tbsp (45mL) freshly squeezed lemon juice (about one medium-large)
- ½ cup (120mL) unsweetened vanilla almond milk
- 1 cup (140g) fresh blueberries
Instructions
- Preheat the oven to 350°F, and lightly coat 9 standard-sized muffin cups with nonstick cooking spray.
- Whisk together the coconut flour, protein powder, xanthan gum, baking powder, baking soda, salt, poppy seeds seeds, and lemon zest in a medium bowl. In a separate bowl, whisk together the coconut oil, egg, and vanilla. Stir in the Greek yogurt until no large lumps remain. Stir in the agave, lemon juice, and almond milk. Add in the coconut flour mixture, stirring until fully incorporated. Let the batter rest for 10 minutes. Gently fold in the blueberries.
- Divide the batter between the prepared muffin cups. Bake at 350°F for 23-26 minutes, or until a toothpick inserted into the center comes out clean. Cool in the pan for 10 minutes before carefully turning out onto a wire rack.









I have now made these, the lemon poppyseed, and the strawberry chia seed muffins. They’re all really great, thank you. I use a little less of a low calorie sweetner (stevia or erythritol) instead of the agave to keep the carbs down and they still work well. Today for the protein powder I tried using half vanilla whey protein and half unflavoured pea protein and that gave an even lighter cakier crumb. Delicioius!
I’m so glad you’re enjoying the muffin recipes Claire! Thank you for sharing your modifications to the recipes. I always enjoy hearing what works! 🙂
Hi Amy! Ive made so many of your recipes and love them ! ? with the recipes that use coconut flour, is the xanthum gum a neccesity or can I omit it?
Thanks for your kind words about my recipes Effe! 🙂 Xanthan gum is what imitates gluten’s structural properties. If you omit it in muffins, they’ll sink while cooling instead of staying tall and puffy, and if you omit it from cookies, they won’t be quite as chewy. I hope you enjoy these muffins if you try them!
I just made these, pretty much exactly as the recipe says, and I love them! I eat pretty much without flour and sugar, so these are the perfect, easy, recipe to use! Thanks Amy!
I’m so glad you enjoyed the muffins Kayleigh! 🙂
What does the xanthan gum do? Is it something to help with the coconut flour?
Xanthan gum is what imitates gluten’s structural properties. If you omit it in these muffins, they’ll sink while cooling instead of staying tall and puffy. I hope you enjoy the muffins if you try them Sarah!
Replaced yogurt with unsweetened applesauce and successfully used plant based protein (just one scoop) these are lovely
I’m so glad you enjoyed the muffins Nicole! Thanks for sharing your recipe modifications — I always love hearing what substitutions work! 🙂
I made these and they were awful. I am an experienced baker, I used the exact ingredients called for and scooped and measured correctly. I kept having to put them back in the oven, and I finally had to take them out. They just never “set” on the inside. The tops looked like yours, but the insides were a weird mushy consistency. I even tried microwaving one the next day, and it was a mess. A waste of ingredients.
Oh goodness! That sounds really frustrating Jennifer. Did you use the same protein powder that I linked to in the Ingredients list? I just made another batch of these yesterday to try to replicate your issue, but since they turned out fine, I’d like to work together to figure out what happened so the strange consistency doesn’t happen again.
These turned out beautifully! Tall and puffy peaks on top. They were so good, even my skeptical husband was impressed. I used Biochem Vanilla Whey protein powder in the same quantity as listed in the ingredients with zero problems. The only sub I made was honey for the agave, and I used fresh blueberries. I will be making these again soon. Thanks so much for sharing!
I’m so glad you and your husband enjoyed the muffins Erin! That’s quite a compliment if even he liked them — thank you so much for sharing that with me! 🙂 I really appreciate that you shared what type of vanilla protein powder you were able to substitute, too. I love hearing what recipe modifications work!
Hi!
I just attempted these muffins and it seems my dough was too dry. Any suggestions? The muffins certainly don’t look like yours lol. Also I’m not a fan of coconut, can almond flour be used in its place?? What about in place of coconut oil?
Thanks!
What brand of protein powder did you use Rose? Typically in this recipe, the brand of protein powder entirely determines whether the muffins turn out perfectly moist and tender or dry and crumbly. For substitutions, use the butter option, as included in the Ingredients list, and you may try substituting almond flour in place of the coconut flour. As I explained in the text of the blog post, coconut flour is much more absorbent than any other flour, so you’ll probably need to add up to 2 or 3 times as much. I’d love to hear how all of these modifications work for you!
Sometimes I get ahead of myself and miss a step when I make something for the first time.. This time I added the whole package of xantham gum (4 tsp!) instead of 1 tsp. This made the batter super thick but I compensated by adding more milk. Used slightly less agave, used MTS vanilla protein. Substituted chia seeds and added at the end with blueberries. They stuck to the pan a little bit on the bottom but turned out ok! I’ll use recommended amount of agave next time.
Yikes! That was some quick thinking on your part Tessa — I’m glad the muffins still turned out okay! I’d love to hear how they turn out the next time you bake them too with the correct amount of xanthan gum and agave! 🙂
It doesn’t get much fresher than this! These little guys look like they are seriously bursting with flavor. Breakfast perfection!
Thanks Karly! 🙂