Three high-protein muffin recipes

They're gluten and grain free, low glycemic and pack 13 grams of protein

Feb 24, 2025

Hi! I’m kicking off the week with three bonus recipes for you, free to all subscribers, and I’m super excited about them.

I spent much of Saturday in the kitchen, testing out different muffin recipes and helping each of my two older kids bake something of their choosing (side note: my middle child has discovered kids’ cookbooks at the library so that has been an adventure! 😉).

I shared this high-protein blueberry muffin recipe on the blog last week, which I turned into three different variations for fun new flavors: lemon poppy seed, cinnamon chocolate chip, and lemon mixed berry.

I don’t know about you, but breakfast can sometimes feel like a struggle for me. There are just so many boxes to check— it has to be quick but satiating, kid-approved but nutrient dense with a good amount of protein.

I think breakfast is my 10-year-old’s favorite part of the day. Maverick is our early riser, often up at 5 a.m., just waiting for me to get up and get breakfast going.

Many mornings, I wake up to “what’s for breakfast, mom?” (nevermind “hi” or “good morning”) followed by a string of his breakfast requests 😵‍💫. They almost always include bacon, omelettes or breakfast burritos. Sometimes this is doable before school (with some pre-planning on my end), but on mornings when it’s not, I have a handful of ideas I turn to. They include smoothies, these high-protein chocolate muffins, and Greek yogurt bowls with fruit, a drizzle of honey and my grain-free granola.

The high-protein muffins have been such a big hit lately (my kids requesting them first thing in the morning and immediately when they get home from school), that I wanted to create different flavors for them, and to share with you!

I’ve tested these several times and have landed on a combination of ingredients that create a low-carb, low-glycemic muffin that still packs a good amount of protein: 13 grams per muffin.

About the ingredients

So where does that protein come from? I used a combination of low-carb and high-protein ingredients like almond flour, lupin flour, Greek yogurt, eggs, and vanilla protein powder to create a nutrient-dense muffin that’s still tender and enjoyable.

Lupin flour, made with lupini beans, is high in fiber and protein. It can sometimes have a bitter taste of you use too much of it, but the sweetener balances it out and lets the other flavors shine. I use Kaizen lupin flour. (You can save 15% with the code StemandSpoon.)

Greek yogurt carries a good amount of protein per serving, but if you need these to be dairy-free, feel free to substitute coconut yogurt (just know that it will lower the protein amount slightly).

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And when it comes to the protein powder, I like vanilla whey protein but you can choose your own favorite! Any powder that is vanilla flavored will add extra sweetness to the muffins so if you choose to use an unflavored protein powder, I suggest increasing the granulated sweetener by 2 tablespoons.

Here is the recipe, friends! I hope you like them and they help answer the always-looming question of “what’s for breakfast?”

The recipe and printable PDF are available below with no paywall. If you like this recipe, I’d be so grateful if you’d tap the ♥️, restack it to share, or forward this email to someone you know who also might enjoy healthy, low-carb recipes.

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Yield: 8-9 muffins

Prep time: 35 minutes

For lemon mixed berry

1-¼ cups almond flour (112 g)
2 tablespoons arrowroot starch (17 g)
¼ cup lupin flour (27 g)
3 tablespoons ground flaxseed meal (22 g)
¼ cup vanilla protein powder (20 g)
2 teaspoons baking powder
¼ teaspoon fine sea salt
½ cup granulated monkfruit sweetener with allulose
3 eggs, at room temperature
½ cup plain Greek yogurt
2 tablespoons extra virgin olive oil
¼ cup unsweetened almond milk
1 teaspoon vanilla extract
1-½ tablespoons fresh lemon juice
1 tablespoon lemon zest
¾ cup fresh or frozen mixed berries (I like a blackberry, blueberry, raspberry mix)

For lemon poppy seed:

1-¼ cups almond flour (112 g)
2 tablespoons arrowroot starch (17 g)
¼ cup lupin flour (27 g)
3 tablespoons ground flaxseed meal (22 g)
¼ cup vanilla protein powder (20 g)
2 teaspoons baking powder
¼ teaspoon fine sea salt
¼ teaspoon ground cardamom (optional)
½ cup granulated monkfruit sweetener with allulose
3 eggs, at room temperature
½ cup plain Greek yogurt
2 tablespoons extra virgin olive oil
¼ cup unsweetened almond milk
1 teaspoon vanilla extract
1-½ tablespoons fresh lemon juice
1 tablespoon lemon zest
2 tablespoons poppy seeds

For cinnamon chocolate chip:

1-¼ cups almond flour (112 g)
2 tablespoons arrowroot starch (17 g)
¼ cup lupin flour (27 g)
3 tablespoons ground flaxseed meal (22 g)
¼ cup vanilla protein powder (20 g)
2 teaspoons baking powder
¼ teaspoon fine sea salt
2 teaspoons ground cinnamon
½ cup granulated monkfruit sweetener with allulose
3 eggs, at room temperature
½ cup plain Greek yogurt
2 tablespoons extra virgin olive oil
¼ cup unsweetened almond milk
1 teaspoon vanilla extract
1 teaspoon apple cider vinegar
½ cup chocolate chips (I like HuKitchen baking chips/dark chocolate gems or any of Lily’s sugar-free chocolate chips)

Preheat the oven to 425°F. Line a standard muffin tin with parchment paper cups (if using a silicone muffin tin, the paper cups are optional).
In a large bowl, combine all of the dry ingredients except for the monkfruit sweetener and any muffin add-ins (e.g. berries/poppy seeds/chocolate). Whisk well to remove any lumps. Set aside.
In a separate medium mixing bowl, whisk together the granulated monkfruit sweetener and the eggs. Add the yogurt, olive oil, almond milk, vanilla extract, and apple cider vinegar or lemon juice. Mix until smooth, then pour the wet ingredients into the dry mixture. Mix until it is well combined.
Fold in the muffin flavor add-ins like mixed berries /lemon zest/ poppy seeds/ chocolate chips. Use a large spoon to spoon the batter into the prepared muffin pan, filling it nearly full.
Transfer to the oven and bake at 425°F for 5 minutes, then turn down the temperature to 350°F and bake for another 16-19 minutes. Remove the pan from the oven and let the muffins cool for 5 minutes in the muffin pan, then transfer to a cooling rack to cool completely.

I like to use a large ice cream scoop to scoop the muffin batter into the muffin pan.
The high blast of heat in the first five minutes of baking will help the muffins rise a little taller, which is especially nice in grain-free baked goods since these alternative flours can lead to a more dense texture.
Lupin flour is made from ground lupin beans, which is a legume that is high in fiber, low in carbs, and high in protein. It adds extra protein to the muffins which is why I chose it for this recipe. It can have a slightly bitter taste- if you taste the batter, you’ll know immediately! However, that bitterness is undetected in the muffins after baking.
I use Kaizen lupin flour. You can save 15% with the code StemandSpoon.
When filling up the muffin cups with the batter, fill them nearly all the way, leaving about 1 centimeter from the top. Low-carb/grain-free flours won’t rise the same way as a wheat-based batter so you don’t have to worry about them overflowing.

Yogurt: For a dairy-free muffin, substitute the Greek yogurt for coconut yogurt or coconut cream. The texture will be the same but your muffins will have slightly less protein.
Olive oil: You can use avocado oil or melted coconut oil instead of olive oil, if preferred.
Sweetener: Use your own favorite low-carb sugar substitute as long as it’s a 1:1 swap for regular sugar. I like granulated monkfruit sweetener with allulose for its clean flavor (no cooling aftertaste like erythritol!). You can also make these with coconut sugar or even regular sugar if you’re simply looking for a grain-free/gluten-free and high-protein muffin recipe.