Surprise the kids with a dollop of jelly tucked inside of these peanut butter and jelly muffins. Be let's be honest, adults love them just as much as the kids do!

Peanut butter and jelly muffin on a white plate.

If there's one thing that disappears in record time in my house, it's muffins. Well, and peanut butter rice treats, too. Neither my husband nor my kids (okay okay, me too) can't keep their hands off of them, which is exactly why I make it a rule to always bake a double batch and freeze the second dozen so that we can have muffins for another day.

While these peanut butter and jelly muffins might not be a good option for school lunch boxes, out of respect for those with nut allergies, they are ideal for after school snacks. Pair it with a banana and you have a quick and healthy breakfast in the making! Try my chocolate chunk banana muffins for a sweet treat in the afternoon.

Tips for making peanut butter and jelly muffins

Be sure to use whole wheat PASTRY flour rather than whole wheat flour. See my notes below for more details and an alternative.
I used smooth peanut butter in this recipe, but chunky would work in a pinch.
When scooping the muffin batter into the muffin tin, I use either a measuring cup or a cookie scoop. Since the batter is a bit sticky from the peanut butter, lightly coat the measuring cup or the scoop with cooking spray so that the batter slides out easily. I do the same with my fingers when poking and prodding the final batter into place over the jelly. Feels a little strange, but it works!

Collage of raw muffins and baked muffin in a muffin tin.

Can you substitute whole wheat flour for white flour in muffins?

A straight one-to-one swap of regular whole wheat flour for all-purpose flour will produce a very dense muffin. There are two possible solutions...

The first solution is to use ½ whole wheat flour and ½ all-purpose flour. While you won't get all of the benefits of white flour, this ratio will produce a more tender muffin than if you used regular whole wheat flour exclusively.
The second option, which is my favorite, is to substitute whole wheat PASTRY flour in a one-to-one swap for the all-purpose white flour. Whole wheat pastry flour contains less protein than regular whole wheat flour, thus producing a more tender product and lending itself to baked goods. All of the nutritional benefits of whole wheat flour with a light texture. A win-win!

A muffin half with jelly in the middle on a white plate.

Other whole wheat muffins recipes

Printable Recipe

Want to save this recipe?

Enter your email below & we'll send it straight to your inbox. Plus you'll get great new recipes from us every week!

Peanut Butter & Jelly Muffins {Whole Wheat}

Snack time! Surprise the kids with a dollop of jelly tucked inside of these peanut butter and jelly muffins.

5 from 1 vote

Print Pin Rate

Course: Breads, Breakfast, Snacks

Cuisine: American

Keyword: Peanut Butter & Jelly

Prep Time: 10

Cook Time: 15

Total Time: 25

Servings: muffins

Calories: 154.9kcal

Author: Dara Michalski | Cookin' Canuck

Ingredients

1 ½ cups whole wheat pastry flour
1 teaspoon baking soda
1 teaspoon salt
¾ teaspoon ground cinnamon
1 egg
¾ cup unsweetened applesauce
⅓ cup pure maple syrup
⅓ cup smooth peanut butter
⅓ cup plain nonfat Greek yogurt
¼ cup strawberry or raspberry jam

Instructions

Preheat the oven to 375 degrees F. Lightly coat a muffin tin with cooking spray.
In a large bowl, whisk together the flour, baking soda, salt and cinnamon. In a separate bowl, whisk together the egg, applesauce, maple syrup, peanut butter and yogurt.
Add the applesauce mixture to the flour mixture and stir to combine. Do not overmix.
Divide half of the batter between the muffin cups. Spoon 1 teaspoon jam into the middle of the batter in each muffin cup. Scoop the rest of the batter over top of the jam, using a small spatula or your fingers to spread the batter so that it covers the jam.
Bake until a toothpick inserted in the center of one of the muffins comes out clean of batter (it may have a little jam on it), 12 to 15 minutes.
Remove the muffins from the pan and allow to cool. Serve or store in an airtight container.

Notes

Please note that I am not a medical or nutritional professional. I provide nutritional information for my recipes as a courtesy to my readers. It is calculated using the built-in recipe card calculator. While I attempt to provide information that is as accurate as possible, you should calculate the nutritional information independently before relying on it.

Nutrition

Tried this recipe?If you make this recipe, I'd love to see it on Instagram! Just use the hashtag #COOKINCANUCK and I'll be sure to find it.

This post was first published on September 6, 2018 and updated on January 28, 2026.

Disclosure: I am a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for me to earn fees by linking to Amazon.com and affiliated sites.

Tips for making peanut butter and jelly muffins