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Home Recipes Healthy Double Chocolate Muffins
GF Gluten-Free DF Dairy Free VG Vegetarian NF Nut-Free

Healthy Double Chocolate Muffins

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Posted:4/28/20
Updated:2/28/22

These double chocolate muffins are going to be your new favorite! They’re easy to make, light and moist, plus they just so happen to be gluten free, nut free and dairy free.

chocolate muffins pinterest

This post is sponsored in partnership with Bob’s Red Mill. As always, all opinions are my own. Thanks for your continued support as I work with brands I not only love and trust myself, but know you will too!

Is there such a thing as too many muffins? I’m going to go ahead and say, “absolutely not.” They’re enjoyed by all and there are so many ways to make them!

I have tons of muffin recipes here on FMK, but up until this point I did not have a standard basic chocolate muffin recipe.

I’ve made this chocolate muffin recipe several times in the last week and a half… and I’m just going to go ahead and say it – they’re the best!!

Chocolate muffins are great because it basically feels like you’re eating dessert for breakfast. Thankfully these ones are a bit on the healthier side using ingredients like applesauce, maple syrup and whole grain gluten flour.

The Best Gluten Free Chocolate Muffins

These healthy chocolate muffins do not disappoint. They’re perfectly moist, light and studded with chocolate chips for the perfect amount of sweetness you want in a muffin.

tipped double chocolate muffin pile

Ingredients List

  • Bob’s Red Mill Gluten-Free 1-to-1 Baking Flour – my favorite gluten-free flour blend! If not gluten-free, feel free to sub whole wheat white or whole wheat pastry flour.
  • unsweetened cocoa powder – make sure to use regular cocoa powder, not “dutch process”. You can also use cacao powder, but the flavor of the muffins may change slightly.
  • espresso powder or instant coffee – this is just a little chocolate flavor enhancer! You can omit if you don’t have any on hand. But if you plan on baking up a chocolate storm, you might as well stock your pantry with it.
  • baking soda & baking powder – using both will get the perfect lift
  • salt – just a touch to help enhance flavor
  • unsweetened applesauce – we’re using a majority of applesauce here that ends up replacing quite a bit of oil in what a traditional muffin recipe might call for. If you don’t have applesauce, well-mashed banana would work too!
  • avocado oil, light olive oil or melted/cooled coconut oil – Use a neutral oil so the chocolate flavor really comes through. If you choose to use coconut oil, make sure the rest of the ingredients used are room temperature.
  • pure maple syrup – using mostly a liquid sweetener for these muffins.
  • granulated sugar – you can use coconut sugar, white sugar, brown sugar or a stevia blend if you’d like. This added granulated sugar helps balance the sweetness of the muffins. If you decide to omit, the muffins will be somewhat bitter.
  • eggs – two eggs here will give you the best texture.
  • vanilla extract – we’re using one whole tablespoon here for a boost of flavor.
  • chocolate chips – OBVIOUSLY we’re adding chocolate chips to these double chocolate muffins. I like to use a mix of regular sized and mini chocolate chips.

Bob’s Red Mill Gluten Free 1-to-1 Baking Flour

This is my go-to flour for all of my whole grain gluten-free baking needs.

Because a lot of traditional baked goods are made with a wheat-based flours, when developing recipes that are gluten-free I always use Bob’s Red Mill Gluten Free 1-to-1 Baking Flour – it has a special blend including xanthan gum, which is perfect for cookies, cakes, brownies, muffins, pancakes and more.

Bob's Red Mill Gluten Free 1-to-1 Baking Flour

Keep in mind that other brands may use different blends of gluten-free flours and starches.

These healthy chocolate muffins baked up so well with this gluten-free 1-to-1 baking flour, I was amazed with the results!

Light, fluffy and simply delicious.

Tips for making healthy chocolate muffins

Here are some baking tips to ensure you get the best possible results with these gluten free chocolate muffins!

chocolate muffins on parchment paper

Mix Wet and Dry Ingredients Separately

To ensure the cocoa powder gets evenly dispersed with the gluten free baking flour, and the leavening agents (baking soda and baking powder), it’s a good idea to mix these dry ingredients together in its own bowl, separate from the wet ingredients.

eggs in mixing bowl with ingredients in bowls

Gently combine

With any muffin batter, you want to make sure you’re not over-stirring.

Once the batter is almost fully combined (with a little bit of dry flour bits remaining) then fold in chocolate chips. As you fold in the chocolate chips, the dry spots should disappear.

chocolate chips in muffin batter bowl

Use a cookie scoop for batter

My medium cookie scoop is one of my most-loved and most-used kitchen tools. From scooping perfectly shaped cookie dough to easily dispensing batter into a muffin tin. If you don’t have one, get one!

muffin batter in tins and Bob's Red Mill 1 to 1 baking flour on towel next to baked muffins

Checking Muffins for Doneness

Chocolate baked goods can be a little tricky. It’s a little bit harder to tell when they’re done due to their already dark color.

Here’s what I suggest:

  • Set the timer on the lower end of the baking time.
  • Check the middle of the muffin with an inserted toothpick for any wet batter.
  • If the toothpick comes out with wet batter, but the tops have domed nicely, pop back in for another 2 minutes – check again.
  • If the toothpick comes out with melted chocolate on it (sans batter), check another muffin and in different spots before deciding if they need more baking time.
cut open chocolate muffin

Recipe FAQs

  • Are there other flours I can sub with? – Your best bet is to use either the Gluten Free 1-to-1 Baking Flour, or sub the same amount of whole wheat white or whole wheat pastry flour. If you’re looking for grain free option (i.e. almond flour) use my paleo chocolate bread and bake in a muffin pan for 15-20 minutes.
  • Can I use mashed banana instead of applesauce? – If you don’t have applesauce, you can sub with the same amount of mashed banana. Just make sure your banana is very well-mashed, or you might need to add a couple tablespoons of milk to help thin out batter.
  • What about using honey instead of maple syrup? – While I didn’t test that myself, I am pretty confident this would work. You might want to increase granulated sugar by another tablespoon or so, though.
  • Do I have to add the granulated sugar? – I highly recommend adding the additional sugar here. It’s needed to get the right amount of sweetness with the chocolate. If you add more maple syrup, the dry and liquid ratios will be off. Also note, if you want a sweeter muffin, I suggest adding about 1/2 cup granulated sugar.
  • How do I make these vegan? – The eggs here do help provide some structure to these muffins. Because these muffins are made with a gluten-free flour blend, I am not certain how using an egg replacer would work out. The muffin texture might be a little more dense. If you try this though, let me know!

Let me know if you make this recipe by leaving a comment and rating below! It helps others learn more about the recipe too! Xx Ashley

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Healthy Double Chocolate Muffins

double chocolate muffin in wrapper
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★★★★★

5 from 10 reviews

These double chocolate muffins are going to be your new favorite! Made with applesauce (or sub mashed banana) a touch of oil to keep them nice and soft, and sweetened mostly with maple syrup. These are TOO good to pass up and no one will know they’re gluten-free and dairy free.

  • Author: Ashley
  • Prep Time: 5 minutes
  • Cook Time: 20 minutes
  • Total Time: 25 minutes
  • Yield: 12 muffins 1x
  • Category: snacks
  • Method: oven
  • Cuisine: American
  • Diet: Gluten Free

Ingredients

Scale

dry

  • 1 cup + 2 TBSP Bob’s Red Mill Gluten-Free 1-to-1 Baking Flour
  • 1/3 cup + 1 TBSP unsweetened cocoa powder
  • 2 tsp espresso powder (instant coffee), see notes
  • 1 tsp baking soda
  • 1/4 tsp baking powder
  • 1/4 tsp salt

wet

  • 3/4 cup unsweetened applesauce
  • 1/3 cup light olive oil (or melted/cooled coconut oil, avocado)
  • 1/3 cup maple syrup
  • 1/4 cup granulated sugar (see notes)
  • 2 large eggs
  • 1 TBSP vanilla extract
  • 1/2 cup chocolate chips (I like to use a mix of mini and regular), plus more for topping

Instructions

  1. Preheat oven to 425ºF and grease muffin pan, or use liners; set aside.
  2. In medium bowl combine dry ingredients – flour, cocoa powder, instant espresso powder, baking soda and salt.
  3. In a large bowl whisk together applesauce, maple syrup, oil and granulated sugar until smooth. Whisk in eggs and vanilla until combined.
  4. Add dry ingredients to bowl of wet ingredients, stirring together gently until almost combined then fold in chocolate chips. Make sure there are no lumpy or dry spots in batter.
  5. Evenly distribute batter into muffin pan, filling about 3/4 way full. Top with more chocolate chips if you’d like.
  6. Bake for 5 minutes at 425ºF, then drop oven temperature down to 350ºF and continue baking for another 9-12 minutes, or until inserted toothpick in center comes out clean (no wet batter). 
  7. Allow muffins to cool in pan for 5 minutes before transferring to wire rack to cool completely. 

Notes

instant coffee – you can omit if you don’t have on hand but it does give the chocolate flavor a boost.

granulated sugar – the additional sugar here helps give these muffins the right amount of sweetness. If you leave out, the muffins will still be a little bitter. If you think you prefer a sweeter muffin, add up to 1/2 cup.

STORING: keep muffins in airtight container at room temperature; best enjoyed within 3 days. 

FREEZING: tightly wrap and store muffins in the freezer, up to 1 month. Thaw in fridge or at room temperature.

Keywords: gluten free muffins, double chocolate muffins

Did you make this recipe?

Tag @fitmittenkitchen on Instagram and hashtag it #fitmittenkitchen

About Ashley

"Ashley Walterhouse is the founder of Fit Mitten Kitchen, based in the Greater Lansing Area of Michigan, AKA “the Mitten.” Ashley grew up as a picky eater but later discovered that eating healthy was actually easy and fun. She started FMK in 2015 as a way to share her newfound love of developing healthier recipes for all to enjoy."

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  1. Gemma's Mom says

    1/17/2022 at 7:37 am

    Fabulous tasting, substituted monkfruit sweetner for sugar, and a pinch (literally) of vinegar for baking powder (allergic to corn). Soy free Chips (Lily’s), and 100% Dutch Cacao. My only problem is they stuck to the cups :(. Next time a little longer cook or to just go 350 the entire time. – Thanks for a great Chocolate treat that fits the Allergan diet!

    Reply
    • Ashley says

      1/17/2022 at 11:07 am

      Hi there, thanks so much for the feedback and sharing your substitutions! Make sure the muffins are completely cool before trying to remove from the liners. I’ve had great success with these specific cupcake liners though. Silicone ones are a great option as well!

      Reply
  2. Alexandra Bucci says

    2/22/2022 at 5:41 pm

    Made exactly as written and we loved them!!

    ★★★★★

    Reply
    • Ashley says

      6/3/2022 at 5:59 pm

      Thank you for your review! So glad you like them 🙂

      Reply
  3. Kathy W. says

    6/3/2022 at 5:51 pm

    These really are the best! My family loved them, and no one could tell they were gluten free. And unlike most gluten free baked goods, they tasted just as good the second day.

    ★★★★★

    Reply
    • Ashley says

      6/3/2022 at 5:59 pm

      Thank you so much for your review! So glad you and the family enjoyed them 🙂

      Reply
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