I’m so excited to share another delicious gluten free muffin recipe with you. Today I’ll show you how to transform simple ingredients you can pronounce into amazing gluten free, vegan, allergy friendly muffins. In addition to being GF, this is a vegan lemon muffin recipe that’s also top 9 free and top 14 free. Whilst it is super duper inclusive, it doesn’t lack in flavour, or in texture. If you share your muffins with your friends, know that these are so good, said friends will absolutely be back for more.
If you’re new to allergy friendly and gluten free baking, be sure to check out my cookbooks, as they can propel you to whole new levels in free-from baking (and cooking). Now, let’s get to work!
Allergy Status
Free From: Wheat/Gluten, Dairy, Egg, Soy, Tree Nut (including Coconut), Peanut, Fish, Shellfish, Sesame, Top 9 Allergens, Top 14 Allergens, Sesame, Alliums, Apple, Avocado, Banana, Beans & Lentils, Berries, Buckwheat, Cane/Refined Sugar, Carrot, Celery, Cinnamon, Corn, Cruciferous, Garlic, Latex Cross Reactive Foods (H/M), Legume, Lupin, Mushroom, Mustard, Nightshade, Oat, Onion, Pea & Pea Protein, Potato (Nightshade Variety), Poultry, Red Meat, Squash & Gourd, Strawberry, Sweet Potato & Yam, Tapioca/Cassava/Yuca/Manioc, Tomato, Yeast
Friendly To: EOE, Vegan
Tools You’ll Need to Make This Vegan Muffin Recipe
- Large Mixing Bowl + Whisk OR Mixing Bowl + Electric Hand Mixer OR Stand Mixer with Wire Attachment
- Kitchen Scale (this is the one that I use)
- Muffin Tin (you can use a 12-cup muffin pan or a mini muffin pan)
- Silicone or Rubber Spatula (I have several of this spatula)
- Zester (if you plan to use the optional lemon zest, this is similar to the zester that I have)
Gluten Free Muffin Recipe Ingredients
Flax Gel/Egg
- 3 TBSP Golden Flax Meal
- 6 TBSP Water (room temperature)
Part 1 Ingredients (Dry Ingredients)
- 130g Organic Maple Sugar
- 60g Brown Rice Flour, superfine
- 60g Sorghum Flour, superfine
- 40g Organic Gluten Free Purity Protocol Oat Flour OR Organic Tiger Nut Flour (tuber, not a tree nut)
- 30g Arrowroot
- 4 tsp Baking Powder
- 1/2 tsp Baking Soda
- 1/2 tsp Sea Salt
Part 2 – 5 Ingredients (Wet Ingredients)
Part 2 Ingredients
- 120mL Milk of Choice (4 ounces)
- 2 tsp Organic Lemon Juice (fresh or from a jar)
Part 3 Ingredients
- 120mL Organic Extra Virgin Olive Oil (4 ounces)
- 1 TBSP Organic Vanilla Extract
Part 4 Ingredient
- 85mL Hot Water (3 ounces)
Part 5 Ingredient
- 2 – 3 tsp Organic Poppy Seeds (I use 8g/2 tsp)
- Optional: 1 TBSP Organic Lemon Zest (to boost the lemon flavour)
Post-Bake Ingredient
- Organic Food Grade Lemon Oil for Brushing
Important Ingredient Notes
Milk of Choice: You can also use any dairy-free milk including oat milk, soy milk, almond milk, homemade milk, etc. The only milk to avoid will be full fat coconut milk from a can. If you’re new to dairy free living, here’s a list of brands that make dairy free milk. If you don’t need a dairy-free option, you can use regular milk (whole milk, sheep’s milk, etc.) in this recipe.
Golden Flaxseed Meal: This is not the same thing as flax seeds, and you need to use “meal” specifically. For best results, use this brand of flax seed meal. Do not swap this for substitutions such as chia seed meal or pumpkin seed meal. Only the flax will work.
Maple Sugar: This is a granulated, unrefined sweetener. It can be swapped for coconut sugar or date sugar. Whilst you could use a different organic sugar such as white cane sugar or light brown sugar, these will read as much more sweet since they’re refined sweeteners. That doesn’t mean you can’t use them, but be sure to manage your expectations. You cannot swap this for a liquid sweetener such as maple syrup, agave, or applesauce (or other fruit puree).
Poppy Seeds: If you can’t have poppy seeds, or just don’t like them, you can leave them out and have epic lemon muffins instead. Be sure to follow all of the other steps, including the lemon oil brushing after baking.
Lemon Zest: This is optional, and can enhance the lemon experience. For something a little different, use orange zest or lime zest in its place.
Lemon Oil: This is NOT the same thing as an extract. If you use extract, you run the risk of ruining your muffins. The oil you purchase needs to be food grade, not what your average essential oils store may sell. I’d link you to the one that I use, but they’ve changed their name and I can’t find them online anymore. I purchase it at a local high quality organic co-op in my area.
Paper Liners: If you like to line your muffin pan like me, you’ll want to use this brand of paper liners. I’ve been using them for over a decade without issue. A good friend shared that not all commercial muffin liners play well with gluten free + egg free baked goods.
Gluten-Free Flour Mix
Let’s take a moment to talk about the flours used in this amazing gluten-free recipe. The best gluten-free muffin recipes start with a foundation of gluten-free flours. If the flour mixture is wrong, the muffins (or other baked goods) will be a hot mess. This is how you get dense muffins, rather than tender muffins.
It’s important to know that different types of flour are going to produce different results (fluffy texture vs dense texture, delicate crumb, etc.). On top of that, how you combine your flour choices will absolutely impact the final results in both taste and texture.
These delicious muffins have a successful gluten-free flour blend, but also functions very well since this is also an egg free recipe. Know that when eggs are involved, you have a little more wiggle room on the gluten free flour front, as the eggs can help you out of a bad situation.
When it comes to swapping the gluten free flours I have listed, there’s not a tonne of space for you to mess about. Usually rice and sorghum are swaps for each other, but since they’re both present, things need to stay as is. I’ve shared an oat swap, and if possible, the arrowroot needs to stay where it’s at. This starch is important for your final texture.
Now, if you have an all purpose flour blend that you’d like to use, you can make that swap. Know that I haven’t tested every gluten free flour mixture on the planet and can’t guarantee your success. I’ve also never worked with 1-1 baking flour type products from Bob’s Red Mill or King Arthur’s Measure for Measure. These 1-to-1 baking flour products contain ingredients I’m allergic to (such as xanthan gum which is corn derived).
What I can tell you about these gluten free all purpose flour products is that they aren’t truly all purpose. They’re most purpose, and it’s up to you to know when they’ll succeed. Some manufacturers tell you on the packaging or the website what the product is really good for. I do have it on good authority from a gluten free only recipe developer (she uses eggs) that commercial gluten free flour blends + almond flour = best baking success. I don’t know the exact ratios, so you’ll need to look into it, assuming you can have almonds.
The most important thing to not do: replace the gluten free flours I’ve listed with one singular flour. If you were to take my blend and swap it all for coconut flour, or brown rice flour only, etc., you will absolutely positively ruin the recipe.
Whilst this recipe is clearly for gluten free muffins, if for some reason you don’t need gluten free, you can use a wheat based all purpose flour (sometimes called regular flour) in place of the rice + sorghum + oat + arrowroot. Don’t use something like whole wheat flour, as it’s not quite the same as an AP flour. Additionally, don’t use something like self-rising flour since this contains a leavening agent, and the recipe already has plenty.
To learn more about choosing flours for gluten free batters, read this article where I do a deep dive on all things gluten free flour.
My Kids’ Favorite Gluten-Free Muffin Recipes
- Simple Gluten Free Maple Muffins Recipe (I’m told these are some of the best gluten-free muffins I’ve ever made)
- Grain Free Pistachio (or chocolate chip) Muffins Recipe (these are fantastic if you like sweet muffins)
- Oat Free, Gluten Free Protein Muffins Recipe
- Chocolate Chia Grain Free Muffins (gluten free, egg free, top 9/14 free)
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Directions for This Gluten Free Muffin Recipe (with pictures)
To make these delicious bakery-style muffins, start by combining your flax meal and water together in a small bowl, and set aside. This is a good time to preheat your oven to 325f/163c, and to get your hot water/kettle going. Now, combine your milk and lemon juice together in a measuring cup and set aside.
Next, place your empty large bowl or stand mixer bowl on your kitchen scale and tare to zero. Add each of the Part 1 Ingredients (dry ingredients) to the bowl and tare between weighted ingredients. Once they’re all in, lightly mix to combine. For this recipe, I use a stand mixer with the wire attachment.
With your mixer on the low setting, pour in your milk and lemon juice combo. Mix long enough to just combine (only a few moments), then turn the mixer off for 1 minute. During this time, the chemical reaction happens, and this will improve the lift.
Whilst you wait, place the (dirty) measuring cup back on the scale, tare, and add the Part 3 Ingredients (oil and vanilla). When the minute is up, add the oil and vanilla combo and continue to mix.
When the oil has been mostly incorporated, turn your mixer off and add the flax gel (sometimes called flax eggs, but I say gel since I use a much thicker bind than other recipe developers). Mix again and you’ll see a thick batter form. Now, add your hot water and mix until a liquid batter forms. Mix on high speed for 30 seconds, then turn the mixer off. Finally, fold in your poppy seeds.
Line a standard sized muffin tin (I use this brand). Use a large cookie dough scooper or ice cream scooper to portion batter into the muffin cups. This batter comfortably makes 12 muffins. With the batter in place, I use a small sieve to sprinkle a little maple sugar on top of each muffin, which is how my kids prefer these gluten free muffins.
Bake at 325f/163f for 22 – 25 minutes. A toothpick should come out clean (a few small crumbs are OK).
You can bake this gluten free muffin recipe as mini muffins as well. Your bake time will be around the 19 minute mark.
When you pull your muffin tin out of the oven, allow the muffins cool in the tray for about 10 minutes before removing. If you wait longer than that to remove your muffins, the paper can start to misbehave from the steaming effect.
Once your muffins have cooled completely, brush the tops with lemon oil for the ultimate lemon experience. Your final results should be fluffy muffins with a cake-like texture and delicate crumb.
Gluten Free Muffin Recipe Storage Notes
You can store leftover muffins at room temp for 4 days OR in the freezer for 4 months.
For counter top storage, I use a clamshell bakery style container. It’s not a perfect air-tight seal… I notice that a perfect airtight seal messes with the moisture and texture a small amount (and it’s exacerbated in some climates and elevations). However, your muffins should not sit completely uncovered.
You can also store your muffins in the fridge, in an airtight container.
To freeze, place cooled muffins on a large baking tray. Put the entire tray in your freezer. Once the muffins have frozen solid, transfer them to an airtight container or freezer baggie. Don’t forget to label with the date and flavor.
To thaw frozen muffins, place your muffins on the countertop for about 90 minutes, or until completely thawed. I don’t recommend reheating from frozen, as this can alter the texture a bit. A friend of mine has done this and says it’s not a big deal, but you know me. I’m all about free-from perfection.
You can also freeze prepared muffin batter, and thaw the batter, then have fresh baked delicious muffins whenever you’re in the mood. I use these deli containers to freeze batters. My free-from batters can be frozen for years (yup, I’ve tested it), and you still get awesome fresh bakes.
Freezing a batter can be helpful if you don’t have a lot of space to freeze complete bakes. It’s also helpful if you still want to get ahead, but don’t like eating leftovers from your freezer.
In my experience, storing leftovers frozen is the best method since you don’t have to remember to eat them by a certain date. Plus, you can batch cook and get ahead.
Serving Ideas
There are quite a few tasty ways to serve your muffins that will give them a little extra oomph. You can totally eat these standalone for breakfast or as a snack, but next time, consider adding a compote made from fresh blueberries, or drizzling melted chocolate chips on top.
You can also serve these delicious muffins with a range of fresh fruit including blueberries, strawberries, bananas, and raspberries. Pretty much anything that pairs well with lemon will pair well with your gluten free muffins.
I’d also like to propose the idea of a delicious yogurt and muffin parfait made with frozen berries. I’m thinking layers of yogurt (or Greek yogurt), frozen wild blueberries (they’re smaller and easier to eat when frozen), chopped muffins (instead of granola), and sliced strawberries. Sounds good, right??
You can serve these gluten free muffins for breakfast, but how about as a breakfast for dinner situation? You could pair these muffins with a dinner protein that pairs well with lemon such as oven baked fish, and have this on the side. Very non-traditional, yet, very delicious.
Meal Prep Tip: Make Your Own Gluten-Free Muffin Mix at Home
If you’ve ever gone to the grocery store and seen gluten free muffin mix in a box and thought, man are these expensive, have I got news for you. You can make the same thing at home, and have bags of muffin mix waiting for whenever the desire to bake strikes.
To make your own “gluten-free muffin mix”, place an empty mixing bowl on your kitchen scale. Add each of the Part 1 Ingredients (Dry Ingredients) one at a time. Don’t forget to tare between weighted ingredients. Give this a mix, then transfer it to a bag, and this is literally what’s in the box mixes sold in stores.
For ease, label the front with the name and expiration date. The date will be based on the dry ingredients you used, Whichever one will expire first, that’s your expiration date.
Print out the Parts 2 – 5 and Post-Bake Ingredients, and tape it to the back of the bag. If you’re a fan of batch cooking or getting ahead in general, you can make 5 bags at a time, so you’re always ready to bake.
I did this ALL the time with muffins, cakes, and brownies so I could easily add the wet ingredients and get to work.
More Great Recipes to Explore
These amazing gluten free recipes are great for the whole family. They’re also super inclusive (gluten free, top 9 free, and more).
- Gluten Free Blueberry Muffins with Pumpkin
- Spinach & Banana Pancakes (gluten free, top 9/14 free)
- Easy Homemade Nut Free Granola Bar Recipe (this is a great recipe for busy mornings, top 9 free)
- Gluten Free, Vegan, Top 9 Free Coffee Chocolate Chip Pancakes
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Answering Your Gluten Free Muffin Recipe Questions
Could I add potato starch to the flour blend?
I don’t recommend adding potato starch. The gluten free flour blend, as is, it top notch. Each time I develop a new gluten free muffin recipe, I create a specific blend to make sure the flavours and texture shine.
Whilst potato starch does add to a delicate crumb, these ingredients are already batting a thousand, so I wouldn’t go fixing something that isn’t broken.
Can I use Stevia in place of the maple sugar?
You won’t be able to use sugar-free options such as Stevia, allulose, monk fruit, and so on. These are all what I like to call special sugars, since they don’t behave like a typical granulated sweetener.
If you need to use Stevia for dietary reasons, I strongly suggest searching online for something like “gluten free muffin recipe sweetened with stevia lemon”. You need to follow a recipe that has the proper ratios in place, to ensure you’ll have success and won’t be wasting expensive ingredients.
Could I use tapioca starch in place of the arrowroot?
For the best muffins, leave the arrowroot in place. If you’re all out or can’t have arrowroot, you can try to substitute with tapioca starch or potato starch. Personally, I’d reach for the potato before the tapioca because it lends to a better crumb. No matter which way you go, be sure to manage your expectations. When you change part of the gluten free flour blend, you will absolutely have different (but still enjoyable) results.
Can I make a poppy free version of this recipe?
Yes! My favorite thing about this gluten free muffin recipe is knowing that it also doubles as a straightforward lemon muffin recipe. Simply skip the poppy seed step and you’re good to go. Don’t forget to brush your muffins with lemon oil once they’ve cooled, as this is a huge part of the great lemony experience.
Can I bake this gluten free muffin recipe at a higher temperature to save time?
No, please don’t try to save time that way (though, I can appreciate when someone is using their time wisely). When you bump up the oven temperature, you run the risk of having the outside cook and set whilst the inside is still raw or under one in the middle. Keep the oven temperature as-is, and don’t skip the step where you cool in the muffin pan for 10 minutes, as this carryover cooking finishes the process for you.
It’s been hard finding gluten free flours in my area. Where I can I purchase high quality options?
I’m sorry it’s been hard finding gluten free flours. Honestly, I haven’t purchased gluten free flour in stores for over a decade. I tend to purchase wholesale (50 pound bags) from brands such as GF Harvest and Authentic Foods. You can also find these on Amazon, along with other quality gluten free flour brands.
Be sure to check out Better Batter, as they have artisan gluten free, and very allergy friendly flours that have been developed by an amazing free-from baker and chef.
Can I swap the maple sugar for honey?
No, you won’t be able to use honey in this recipe. Maple sugar is a granulated sweetener (grain-like). Honey is a liquid sweetener (like maple syrup and agave). When swapping, you have to swap granulated for granulated and liquid for liquid. If you were to use honey in this gluten free muffin recipe, you’d ruin it.
Will coconut oil or vegan butter work in place of the olive oil?
No, coconut oil, and dairy free butter (melted or whole) won’t work in place of the olive oil. Butter and coconut oil are solid at room temperature, which is great for some applications such as cookies. Olive oil on the other hand is liquid at room temperature. This allows for a soft texture with additional moistness, even after its cooled. When you use something like coconut oil or butter, once the muffins cool, the texture won’t be right.
Olive oil is the top choice, followed by tiger nut oil (tuber, not a tree nut). You could use other oils, but you’ll want something that has a. neutral flavour.
Do I need to cool my muffins on a wire rack?
No, in fact, it’s important that you leave the muffins in the baking tray for 10 minutes. The tray cooling method taps into “carryover cooking”. It’s where we take advantage of the residual heat in the muffin tin to continue to bake the muffins. In gluten free + vegan + free-from baking, this is a huge part of the baking process.
A cooling rack has no heat, and introduces more air flow, which can rapidly cool your muffins. We don’t want that, so, with this gluten free muffin recipe, keep them in the tray for 10 minutes, then eject.
Can I use buttermilk in place of the milk and lemon juice?
Technically, yes, you could use buttermilk in place of the Part 2 Ingredients. However, if you use buttermilk, you’ll miss out on some of the lemon flavor. Additionally, buttermilk isn’t an ingredient I’ve ever worked with before (one of my kids is allergic to milk). So, I can’t guarantee that it will actually work in this scenario, hence, technically. Milk + lemon juice is one of the top substitutions for buttermilk, which is why it should work just fine.
If you choose to go this route, consider adding extra lemon zest in the mix so you don’t diminish the lemon flavor.
Could I add blueberries and have lemon blueberry muffins?
Maybe. Fruit + free-from muffin batter is always going to be a delicate situation. The water content of your blueberries can throw off the recipe and you may not love the lemon blueberry muffins.
If you wanted to use this recipe for that purpose, I suggest purchasing organic frozen wild blueberries. They’re much smaller than standard blueberries. Make this gluten free muffin recipe, then portion 6 muffins as you normally would into your muffin tin (about half the muffin batter). Now, place blueberries on a cutting board or a piece of parchment paper. Dust with a teaspoon or two of gluten free flour and mix. Coating your frozen fruit in flour will help it better integrate into the muffin batter.
Gently add the blueberries, along with another Tablespoon of maple sugar to balance the sweetness. Fold in your blueberries and sugar, then transfer the lemon blueberry muffin batter to your muffin pan. Start with the regular bake time, then see if your lemon blueberry muffins can pass a toothpick test.
In terms of how much blueberries to use… you don’t want to use so much that the sweetness of the recipe is thrown off. You also don’t want to use so much that it’s blueberry overload. Personally, I’d start with a US dry half cup measurement and see if that’s a good amount.
Are there mix-ins I can add to these muffins to make them different each time?
Honestly, I’m not sure. I’m going to give you a solid maybe. Gluten free + egg free baking is a delicate endeavor, so adding mix-ins has to be done with a lot of thought and care. You could try dried fruit such as cranberries (I don’t suggest raisins as the flavors may clash), or pieces of dried fruit such as mango.
Shredded carrots or shredded zucchini could be very interesting mix-ins, but you’d have to squeeze them super dry and mind the water content.
I’d avoid freeze dried fruit as a mix-in, as it will absorb liquid from your batter and throw things off. You could look around online to see what other recipe developers are using for mix-ins to get better ideas. Just be sure to keep sweetness levels in mind, water content, and how the flavors will interact.
