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Lemon Berry Quinoa Flour Muffins

Are you looking for healthy quinoa flour recipes? These nut free Lemon Berry Quinoa Flour Muffins are a tasty, flour less option for a nutritious and easy breakfast on the go or a gluten free snack for school or work.

Fresh baked muffins on a wooden surface with a lemon in the background

My first taste of these Lemon Berry Quinoa Flour Muffins was pure bliss.

Earthy, creamy, sweet and satisfying are all great descriptors.

When I was in the middle of my Master Cleanse, I was blogging about Cream Cheese Stuffed Carrot Cake Muffins . It was self inflicted cruel  and unusual punishment and I became obsessed.

I could not wait for the cleanse to be over so I could make muffins.

I plotted, planned, researched … what kind of muffins?



What kind of flour?


Something gluten free?

I painstakingly prepared for these muffins like the crazy OCD lady I truly am. These beautiful babies are the result.

They are so lovely and lemony fresh. Who’s in?!

lemon zest in a white ramekin with a zested lemon and zesting tool in the background

I have heard about using quinoa flour in baking for a new gluten free option and I was excited to try it.

And I mean I was really exited to try it. You know you’re a food blogger when trying out a new flour results in a giddy kitchen dance and you actually take a photo said flour bag.


quinoa flour package with lined muffin tin in the background


When I whisked the dry goods together I really caught the aroma of quinoa.

It was a bit bizarre.

The quinoa flour seemed pretty flat and fine.

Before adding in the organic cane sugar, I rubbed in lemon zest to add a citrusy flavour.

muffin ingredients and lemon zest in a white mixing bowl

This brand of organic berries was on sale at Fortino’s so I stocked up on a couple of bags and am looking forward to using them up.

It has cherries, blackberries, and blueberries.

frozen berry package
frozen berries being stirred into muffin batter by a wooden spoon

I added in a touch of sweetened cream cheese to the center of each muffin.

I used less cream cheese than with the carrot cake muffins. With the carrot cake ones I wanted to emulate the thickness of the typical cream cheese frosting and with these I just wanted to add a touch of creaminess.

I sweetened the cream cheese with a bit of sugar and lemon zest.


I filled the muffin cups 1/2 way, added about a teaspoon of the cream cheese mixture, then topped them off with the rest of the muffin batter.

I found the quinoa flour yielded a little less than my usual spelt flour and making a dozen resulted in smallish muffins.

Because of this I recommend only making 10 muffins so they are a little larger than the ones I made.

a hand holding a half eaten Lemon Berry Quinoa Flour Muffin

The verdict is an enthusiastic thumbs up!

I quite enjoyed the sweet, citrusy flavour. It was a nice switch up from the usual chocolate or peanut butter.

I also liked the quinoa flour for baking.

The muffins had a nice crust on the top and there was a faint taste of quinoa which gave them a slight earthy sweetness. It’s nice for those with coconut allergies to have another gluten free option besides coconut flour.

Good stuff. πŸ™‚

Fresh baked Lemon Berry Quinoa Flour Muffins on a wooden surface with a lemon in the background



Carrot Date Muffins

Pineapple Ginger Muffins

Carrot Cake Spelt Flour Muffins

Peanut Butter and Dark Chocolate Breakfast Muffins

Carrot Ginger Raisin Muffins

Cream Cheese Stuffed Carrot Cake Muffins

Be sure to follow me on social media! I love pinning to Pinterest, sharing on Facebook and posting pics to Instagram. See you there.  πŸ™‚

Originally posted in October 25, 2013. Updated May 24, 2020

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I use stainless steel muffin tins for this recipe.

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Quinoa Flour Muffins – Lemon Berry

Sharon Rhodes
Are you looking for healthy quinoa flour recipes? These nut free Lemon Berry Quinoa Flour Muffins are a tasty, flour less option for a nutritious and easy breakfast on the go or a gluten free snack for school or work.
3.66 from 23 votes
Prep Time 10 minutes
Cook Time 20 minutes
Cool 10 minutes
Total Time 40 minutes
Course Dessert, Snack
Cuisine American
Servings 10
Calories 192 kcal



  • Preheat oven to 400 and line a muffin tin with paper liners
  • Whisk together the quinoa flour, salt, baking powder, and cinnamon in a large mixing bowl
  • In a separate bowl, add the sugar and lemon zest and rub them together. I just used my fingers! Add to the flour mixture and stir.
  • In another bowl, mix olive oil, egg, milk, and vanilla.
  • Combine the wet ingredients into the quinoa flour mixture, adding it bit by bit until just combined. Then fold in the frozen berries.
  • Stir together the cream cheese, lemon zest, and sugar. Fill each muffin cup half way with batter and then add a teaspoon of cream cheese filling to each. Finish with the remaining batter so you can’t see the cream cheese filling.
  • Bake muffins for 20 minutes, or until muffins are golden brown and a toothpick comes out clean.
  • Let cool on a wire rack.
  • Store covered for up to 2 days.


Calories: 192kcalCarbohydrates: 24gProtein: 3gFat: 8gSaturated Fat: 1gCholesterol: 21mgSodium: 29mgPotassium: 132mgFiber: 1gSugar: 13gVitamin A: 100IUVitamin C: 0.7mgCalcium: 67mgIron: 1mg
Keyword lemon berry quinoa muffins, quinoa flour muffins
Tried this recipe?Let us know how it was!

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  1. Hi Sharon,
    I tried making the quinoa flour lemon blueberry muffins and I don’t know if I didn’t understand the instructions but where does the lemon zest/sugar combo go? There’s one part that says add to flour mixture then another part says mix with cream cheese. Which one is it?
    Also I didn’t find 1 1/2 cups quinoa flour made a lot of batter. Am I missing something?

    1. Hi Theresa! The lemon zest + sugar combo is mixed with the flour mixture. There is a separate tsp of lemon zest listed in the ingredients at the bottom with a tbsp of sugar to go with the cream cheese mixture. And yes, it doesn’t make huge muffins for sure. The quinoa flour is pretty dense and they are not like cake-y white flour muffins at all. Hopefully, that helps. This is a pretty old recipe and I could definitely update the instructions so it is more clear. Thanks for pointing it out! Much appreciated.

  2. 4 stars
    This smells absolutely heavenly! First time baking with quinoa flour. I followed everything, except I used Monk Fruit/Erythritol instead of sugar cane. and only used half as much sweetener. Why is there a bitter aftertaste? πŸ™ It’s healthy and it’s a great alternative to dessert, so I’m willing to ignore the aftertaste for now. But did I do anything wrong? Or is the bitterness inherent to the quinoa flour?

    1. I don’t find it bitter myself but I’ve never used those substitutions. Do you use the monk fruit/erythritol combo in other baked goods? Does that have an aftertaste?

  3. So this was my first recipe using quinoa flour, quite a distinctive flavor it has, not bad, just different, earthy… I used strawberries instead of berries, didn’t have any on hand. They taste good, some bitter, is that normal? Is that the taste of the flour, since it was my first time using it, I didn’t know what to expect:)), but I really like the recipe, it turned out perfect, not too dry or too wet! Thank you for such a great recipe!

    1. I also find the flavour of quinoa flour earthy! I enjoy it. I don’t notice any bitterness but I know that not rinsing quinoa well can leave it bitter. Perhaps your flour wasn’t rinsed well before it was ground? You can also make your own! I’m planning a post soon. πŸ™‚ Have a great weekend Alina!

  4. Hi Sharon I just made these. They came out great. I used cupcake tins since that’s what I have. I filled them up. Could you tell me how to keep them fresh. Not that I think they will last that long. But I’m hoping to keep some for breakfast in the go or a midday snack at work. Do they need to be refrigerated since they have cream cheese in them ? Thanks for a great recipe Catherine

    1. Hi Catherine! I would keep them in a sealed container in the fridge for optimum freshness. πŸ™‚ So glad you enjoy them! Have a great Sunday.

  5. I live your recipe, thanks so much for sharing it πŸ™‚ I twisted a little using pineapple instead. I didn’t have any berries. My husband and I love them!

  6. I made this today and they came out great!
    I used normal milk, since I didn’t have any almond milk. And I used Greek yogurt instead of cream cheese, and mixed in.
    I used coconut oil, instead of olive oil.
    The batter was a bit dry, more like a cookie batter.
    I will definitely make them again!
    Thank you for a great recipe!

  7. I Should clairify haha, I mixed the applesauce all together into the batter (I didn’t plop it into the batter like the directions for the cream cheese)

  8. The muffins turned out good! I have a dairy intolerance so I substituted the 3 tablespoons of cream cheese and used unsweetened applesauce instead.

    1. Thanks so much Janelle! Love the applesauce swap, too. A good substitute to lighten these up also! πŸ™‚

  9. I’m 52, been baking most of my life-followed this recipe-I get pie crust consistency, not batter. Am I missing something??

    1. Hey June! I’m so glad you enjoyed this recipe. Quinoa flour opens up a whole new world! πŸ™‚ Happy new year.

  10. Thank you so much for this recipe! I have been looking for a good recipe that I could make allergy-friendly for a lady at our fellowship. This is now my go-to recipe. I have never used quinoa flour and didn’t know what to expect but the texture of these muffins was just phenomenal.

    I had to make a few adjustments to make these egg and dairy free (and I didn’t have a few ingredients so had to make do). I’d like to share for those in the same boat.

    1. Egg substitute: 1/2 banana, smashed well.
    2. I used coconut oil instead of olive oil and just mushed the solid coconut oil into the banana.
    3. Had to add more almond milk as there was not enough liquid (probably should have melted the coconut oil first…)
    4. Maple extract because I didn’t have vanilla
    5. No berries and left out cream cheese.

    This made a VERY flavorful basic muffin with a lovely kind of almost caramelized crust.

    Again, thank you so much. It means a lot to my friend when she has something she can eat at our weekly gatherings. There are also others with food allergies/sensitivities who will love them too.

    1. I agree with you on the caramelized crust! It’s so nice. Thanks so much for the great suggestions. I’ll be trying those out myself. πŸ™‚ You are a very kind person to think of others, both by making these for your friend and to take the time to share your version of it for vegans here. The world needs more Dawns! Thanks again. πŸ™‚

      1. Aww shucks… thank you! I know how hard it is to eat in this world when you can’t have what everyone else has (my daughter and I are gluten sensitive and my son is sensitive to all kinds of stuff so I read labels and learn to substitute a lot! Plus we really try to eat “real food” and our extended families…not so much). I try to “do unto others” as best I can!

        1. I like the ‘others’ concept. πŸ™‚ I guess if there is an upside to gluten sensitivities, it is freshly prepared meals from whole foods.

    1. I have never tried freezing these. We typically eat the batch! πŸ˜‰ I’m fairly sure they would freeze fine though. Thanks Margo!

  11. Thanks for the recipe! I just prepped the dry ingredients as I have a gf buddy coming for a visit in the morning.

    I’ve never heard of using olive oil in a muffin recipe…I suppose that canola oil would be a good 1:1 substitute.

    Oh, and I only have mascarpone cheese, which I assume could sub in for cream cheese…

    I’m sure it will work out well! Thanks.

    1. The mascarpone will taste amazing! πŸ™‚ I use olive oil as it has more nutritional benefit than the canola but it should work just fine. You’re a nice friend to bake muffins! Have a great time. πŸ™‚

  12. Can you make these without the cream cheese center all together? I haven’t seen a clear reply to that question… Thanks!

    1. Sure! The cream cheese adds a nice tang and creaminess but is not a requirement. πŸ™‚ Maybe replace it with a bit of butter or oil to keep it moist.

  13. Great news! Daiya now makes cream cheese! No soy, no dairy. Tapioca-based.
    It tastes GREAT and has the right consistency.
    They make cheese, too–and PIZZA, although I haven’t found that yet.
    All I can say is yum yum yum.
    P.S.–Just tried Earth Balance –great substitute for butter, but it has soy. πŸ™

    1. I am also not down with soy. Organic dairy works for me, but Daiya is a great brand for vegans. Cool they have a cream cheese now!

      1. Trying to find easy way to grind quinoa into flour for muffins ( p.s do all quinoa muffin recipes have to use and additional flour beside quinoa and any heart healthy quinoa muffins which contain no sugar or butter?) and possible make noodles.

        Saw a mention of Ninja. Did it work? What type of Ninja as they’re are a few models and packages some of which comes with drink vessels which have a ninja blending top with a blade, a food processor bowl, or a blender container?

        cheers, tess

        1. Hey Tess! I can’t really speak to the Ninja as I don’t have one, but I do know that people have had success using a coffee grinder to process quinoa into flour. I plan to try that method out soon.

  14. Looks and sounds amazing! Would love to try but what can I substitute for cream cheese? I can’t use the Toffuti cream cheese either.

    1. Hi Galit! Thanks for checking out the site πŸ™‚ Either butter or (if you are vegan)Earth Balance in place of the cream cheese would taste delicious. Happy New Year!

  15. I’ve made my own quinoa flour by grinding whole quinoa in my vitamix…you might not be able to do it in a regular blender though, a high-power blender like a vitamix or blendtec is key.

  16. I’d love to try these. I just learned I have to be meat,wheat,and dairy free. Plus, grains only once in awhile. I seem to be fine with spelt and almond flour. I don’t have quinoa flour, just the grains. Could I grind it like I do almonds? Any suggestions? It’s so hard to follow this but my immune system was so compromised by wrong eating, I’m willing to follow. I feel fabulous now, but am so tired of fish and veggies. No peppers, tomatoes, cabbage, eggplant. Other than that, all other veggies and fish. No tropical fruits, but I can have all the others. Would love a sweet and this has all I can have except no cream cheese. So I’m thinking I’ll try w/out it. Any suggestions?

    1. Hi Hilary! Thanks for checking out my site πŸ™‚ As far as the flour goes for this recipe you could totally use both spelt or almond flour instead of the quinoa flour. I don’t know about grinding the quinoa itself into a flour. I’m curious now if that’s all you’d have to do … I will investigate! I feel for you with all the restrictions to your diet. I hope you will be able to find some more recipes here that suit your lifestyle!

  17. That looks delicious!!! I felt like I could taste your muffins when I saw the lovely combo of the sugar, blueberries, and lemon!! πŸ™‚

  18. I totally love that I’m not the only person out there who would do a little jig over something like trying a new flour! Gorgeous photos – love that distressed black wood which totally shows off the food! And … Mmmmmm … the recipe sounds fantastic, especially with the hidden treat of yummy cream cheese. πŸ˜€ Perfect!

    1. Thanks Shelley! I have a friend at work that is our kindred spirit … he loves trying new flours. When I was in BC this summer I bought him a little sack of organic yellow pea flour and he was so excited! I just enjoyed the fact is is called yellow.pea.flour πŸ˜‰ And you know what else is funny? The background of this photo is actually a placemat πŸ™‚ I’m glad it looks like real wood.

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