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Peanut Butter and Jelly Mini Muffins

Peanut Butter and Jelly Mini Muffins are healthy sweet treats made with banana, peanut butter, quinoa and almond flours for a gluten-free breakfast or snack.

Muffins are such an ideal food. They're a little sweet, easy to take on the go, and work for breakfast or an anytime snack. While store-bought muffins tend to be fully loaded with sugar and added fat and oil, it's so easy to make homemade muffins with healthy ingredients.

And still, you can use your favorite flavors! These peanut butter and jelly mini muffins are full of real peanut butter flavor with plenty of protein and fiber from gluten-free flours.

collage of the steps to make pb&j muffins in a mixing bowl

How to Make Gluten-Free PB&J Muffins

I like to break this recipe down into wet and dry ingredients. In one bowl, combine the wet ingredients:

  • An egg, which adds protein and helps the muffins rise.
  • Mashed bananas. Make sure they're nice and ripe for the best flavor.
  • Peanut butter. Use creamy for the best texture in your muffins.
  • Almond milk. Or any other dairy-free milk.
  • Maple syrup. I highly recommend using maple syrup for its caramel-like flavor. However, honey or agave will also work.

Then, in a second bowl, combine your dry ingredients:

  • Oat flour. I recommend using store-bought oat flour rather than making your own in a food processor. It doesn't get as fine and easy to mix in a food processor.
  • Quinoa flour. This has a ton of protein. But don't worry your muffins won't taste like quinoa.
  • Coconut sugar. You can also use granulated sugar if that's what you have.
  • Baking powder and salt

Then, for the jelly part of these peanut butter and jelly muffins, swirl in your favorite strawberry jam and more peanut butter. When the mini muffins bake, they'll have a gooey PB&J center that oozes out. SO good.

overhead of mini peanut butter and jelly muffins in a mini muffin tin before baking

Can I Make Bigger Peanut Butter and Jelly Muffins?

Certainly. I like to make these in a mini muffin tin because they make a nice light snack. For breakfast, however, you might want something more filling. You can make the muffins in a 12-cup muffin tin. Just add 5-8 minutes to the cooking time.


You can make peanut butter and jelly mini muffins for breakfast meal prep. Store them in an airtight container on the counter for 3 days, in the fridge for 5 days or in the freezer for up to 3 months.

You can reheat each muffin in the microwave or slice and toast if you like crispy edges.

close up of mini muffin with peanut butter & jelly swirl on top

Can I Use A Different Nut Butter?

Yes. If you want a peanut-free version of these nutty muffins, feel free to use creamy almond, cashew or sunflower seed butter.

More Muffin Recipes

If you make these Peanut Butter and Jelly Mini Muffins, be sure to tag me on Instagram and leave a rating and review below–I love hearing what you think!

Peanut Butter & Jelly Mini Muffins

5 from 3 votes
Peanut Butter and Jelly Mini Muffins are healthy sweet treats made with banana, peanut butter, quinoa and almond flours for a gluten-free breakfast or snack.
author: Alyssa
yield: 36 mini muffins
overhead shot of mini muffins with peanut butter and jelly on top
Prep: 5 minutes
Cook: 12 minutes
Total: 17 minutes


wet ingredients:

dry ingredients:

add ins:


  • Heat the oven to 350ºF. Grease a 24-cup mini muffin tin and set aside.
  • In a small bowl, beat together egg, banana, peanut butter, milk, and syrup.
  • Add the dry ingredients directly into the bowl with the wet and stir to thoroughly combine.
  • Fill each cup 3/4 of the way full. Add 1/8 teaspoon strawberry jam and 1/8 teaspoon creamy peanut butter into the center of the muffins. Swirl it around with a toothpick. Repeat with the remaining muffins.
  • Bake on the center rack for 12- 14 minutes until a cake tester inserted into the center comes out clean.
  • Cool in the pan for 2 - 3 minutes, then transfer to a wire rack and cool completely. Resist the urge to not break into them; cooling them will allow everything to set properly. If desired, reheat in the toaster oven or in the microwave.



Serving: 1muffin | Calories: 101kcal | Carbohydrates: 12g | Protein: 3g | Fat: 5g | Saturated Fat: 1g | Trans Fat: 1g | Cholesterol: 5mg | Sodium: 51mg | Potassium: 83mg | Fiber: 1g | Sugar: 3g | Vitamin A: 8IU | Vitamin C: 1mg | Calcium: 34mg | Iron: 1mg
cuisine: American
course: Breakfast

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13 comments on “Peanut Butter and Jelly Mini Muffins”

  1. Pulling 2nd batch out of oven now, so making twice in a week’s time says good things. For those who use more conventional store items the squeezable peanut butter and grape jam that is heated in a ziplock bag, corner clipped off, make for a much faster topping application. Natural peanut butter having a runnier texture and likewise the homemade jam per video would appear to lead to the visual results in photos on website.

  2. I’m having trouble finding quinoa flour. Can I use whole wheat pastry flour or more oat flour? What is the best substitute?

  3. Hi Alyssa,
    I am making the PB&J mini muffins and in the instructions you mention vinegar, but it’s not listed in the ingredients. Is this a typo? Or is there actually vinegar in the recipe? If so, how much? Thanks!

  4. Avatar photo
    Silvia Camarillo

    My daughter would love these but she’s allergic to egg, any suggestion to replace egg in this recipe?
    Thank you!

    1. Avatar photo
      Teagan Mosenthal

      Hi Silvia! Without the egg, they might have trouble rising. But you could try a flax egg if you’re okay with a different consistency! Let me know how they turn out if you do try it!