Healthy Blueberry Lemon Poppy Seed Protein Muffins | Amy's Healthy Baking (2024)

Healthy lemon poppy seed muffins with fresh blueberries and a big protein boost! These practically taste like cupcakes for breakfast!

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!