These gluten free peanut butter chocolate chip muffins are the perfect balance of peanut butter flavor. Just enough to taste it, but not so much that it overwhelms the chocolate. They are gluten and dairy free, incredibly simple to throw together, and work just as well for breakfast as they do for an afternoon snack or a little dessert after dinner.

Gluten free peanut butter chocolate chip muffins on a counter with one cut open to show texture.

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Muffins are always a favorite at my house. I have been making gluten and dairy free muffins for years, and I like to keep them as easy as possible with ingredients I always have in the pantry.

They also have to pass the kid test. My boys are picky, but they always need a filling snack for baseball practice or a long tournament day, so easy make-ahead breakfasts show up a lot around here. The kids and I are always rotating between these beauties, my gluten free lemon muffins, gluten free blueberry waffles, or chocolate chip baked oats on the go.

This particular recipe came from my eleven year old requesting a peanut butter muffin. He knew exactly what he wanted, and he was right. These muffins are filling, naturally sweetened with maple syrup, and bake up with cute soft, pillowy domes on top. Once you try them, you’ll see why they’ve become a staple in our rotation.

Why You’re Going to Love This Recipe

Kid-approved and freezer-friendly.
Just enough peanut butter flavor and the perfect texture.
Super simple ingredients and easy to mix up in minutes.

Labeled ingredients for gluten-free chocolate chip muffins on counter.

Ingredient Notes

Ground Flax Seeds – Make sure you’re using ground flax (also called flaxseed meal), not whole flax seeds. I like golden for best color, but the brown or golden color will work. If you only have whole seeds, you can grind them in a coffee grinder.

Milk – You can use any type of milk, dairy or non-dairy. I typically use either homemade cashew milk, or store bought, Elmhurst brand cashew milk.

Peanut Butter – Use an all natural, smooth peanut butter that’s well mixed. I used salted peanut butter. If yours is unsalted, you may want to use ½ teaspoon of sea salt in the recipe instead of ¼ teaspoon.

Chocolate Chips – I typically prefer the mini chips in muffins, but you can use whatever you like. I love the Enjoy Life Semi-Sweet Chocolate Chips.

Full ingredient list can be found in the recipe card below.

How To Make Gluten Free Peanut Butter Muffins

Preheat the oven to 350°F. Line a muffin tin with parchment cups and lightly spray with non-stick spray if desired (helps prevent sticking).
In a medium mixing bowl, whisk together the almond flour, flax seeds, baking powder, and sea salt. Set aside.
In a large mixing bowl, whisk the eggs, maple syrup, vanilla, and milk until smooth. Add the peanut butter and whisk (or beat with a hand/stand mixer) until fully blended.
Add the dry ingredients to the wet ingredients and stir until well combined.
Fold in the chocolate chips.
Divide the batter evenly among the 12 muffin cups.
Bake for 18 – 20 minutes, until the muffins are lightly golden on top, domed, and a toothpick inserted in the center comes out clean.
Let muffins cool in the pan for 10-15 minutes.

Two photos to show the tops of gluten free peanut butter muffins, including fresh baked in muffin tin and on counter.

Jen’s Recipe Tips

This recipe can be made with a whisk in a bowl, but if you have arthritis, or just want it a bit easier, a stand mixer with a whisk attachment, or electric beaters make it easier to blend the wet ingredients.
Don’t take the muffins out of the oven too early or they will be a bit dense and sink when you take them out.
Store in an airtight container in the refrigerator for 3-4 days, or freeze for 2 months. You can reheat in the microwave for 20 seconds or so.

Stacked gluten-free chocolate chip muffins on counter with chocolate chips.

Nightshade free tacos with ground beef inside corn shells standing up on counter.

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