Low Carb Lemon Chia Seed Muffins

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Low Carb Lemon Chia Seed Muffins made with coconut flour are the perfect low carb muffins. They are moist, packed with lemon flavor, and have only 5 net carbs per serving.

154 CAL 10g CARBS 10g FAT 6g PROTEIN

These Low Carb Lemon Chia Seed Muffins are the perfect treat when you are craving baked goods on a low carb diet. Made with coconut flour, these muffins are easy to make and full of flavor.

One of the hardest things about eating low carb is leaving behind the bread and baked goods. That's where low carb muffins come into play.

When you have a serious hankering for a baked good, make these simple low carb lemon muffins instead. With just 5 net carbs per muffin, they are a guilt-free treat that works for almost any low carb or keto diet.

I was so excited to try out these muffins when I first saw the recipe on Slim Palate. Not only am I a sucker for a low carb muffin, I also love anything lemon flavored so these were right up my alley.

Plus I love the using chia seeds instead of the poppy seeds to add some extra protein and fiber. They make a great breakfast on the go or afternoon treat with coffee.

Let's talk about the texture of these muffins. Since we are using coconut flour, they won't be as light and airy as a normal muffin. They will be really moist and a little denser than a typical muffin.

Personally, I love that and it reminds me of really moist banana bread. They also aren't overly sweet.

If you like a sweeter muffin, you will want to use more liquid Stevia to get more sweetness. Experiment with the amount until you hit the sweet spot for your palette.

Also if you are like me and always wondering how you can personalize a recipe, these low carb muffins can be made with all types of citrus.

So far I have also made them with lime juice and lime zest and we loved it. Turned out kind of like a key lime pie flavor, especially if you use some extra vanilla extract. Orange and grapefruit are next on my list.

Low carb muffins with lemon and chia seeds on a wooden cutting board.

What is coconut flour? Is coconut flour low carb?

Coconut flour is flour made with dried coconut meat that has been dried. It is naturally gluten-free and low in carbs. Plus it has more fiber and protein than standard flour.

This makes it popular for baking in the paleo, low carb, and keto communities. Specifically, coconut flour has 120 calories per 1/2 cup serving.

In that half-cup serving, there are 16 grams of carbs, 10 grams of fiber, 4 grams of protein, 4 grams of fat, and just 2 grams of sugar. That means it has just 6 grams of net carbs per serving.

Can I freeze these lemon low carb muffins?

These low carb muffins can be popped in the freezer for up to three months. Normally I make a double or triple batch and place the leftovers in the freezer for quick breakfast and snacks.

To defrost, you can either take them out and leave them in the fridge overnight.

Additionally, you can wrap the muffin in a moist paper towel and microwave from 60-90 seconds. Lastly, you can put them in the toaster oven until they are just heated through.

What to serve on a low carb muffin?

There are lots of options for topping a low carb muffin. The most popular is butter since it is the classic option for muffins. This is delicious with these muffins if you pop them in the toaster first.

Almond butter or cashew butter is another good option plus it adds protein and healthy fat.

You can also use a low sugar jam. These lemon muffins are really tasty with a low sugar raspberry jam. Some people also like to top their muffins with a small amount of yogurt.

Can I use almond flour instead of coconut flour?

Almond flour and coconut flour are not interchangeable when it comes to baking. They bake differently and absorb liquid very differently. This means you can't just substitute one for the other in low carb baking.

The Recipe
Low Carb Lemon Chia Seed Muffins

Low Carb Lemon Chia Seed Muffins

Adapted from slimpalate.com
154 CAL 10g CARBS 10g FAT 6g PROTEIN
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  • 1/2 cup coconut flour
  • 2 tbsp. chia seeds
  • 1/4 teaspoon baking soda
  • 1/16 tsp. salt
  • 1/2 cup unsweetened almond milk
  • 4 eggs
  • 2 lemons (zest of both and 2 tbsp. juice)
  • 2 tbsp. coconut oil melted
  • 1 tbsp. apple cider vinegar
  • 1/2 tsp. liquid stevia (or 3 tbsp honey for Paleo)
  • 1/4 tsp. vanilla extract

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Preheat oven to 350 degrees.


In a medium bowl mix together the coconut flour, chia seeds, baking soda, and salt.


In another bowl, whisk the eggs with the almond milk. Stir in the lemon zest, lemon juice, apple cider vinegar, coconut oil, Stevia, and vanilla extract.


Add the wet ingredients to the dry ingredients and stir until well combined with no lumps. Pour into a muffin tin sprayed with cooking spray or lined with cupcake liners.


Bake for 20-25 minutes until fully cooked. Let cool for at least 10 minutes.


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Nutritional Facts
Serving Size: 1 muffin
Amount Per Serving
Calories 154
Calories from Fat 92
% Daily Value *
Total Fat 10g
Saturated Fat 5g
Monounsaturated Fat 0g
Polyunsaturated Fat 0g
Cholesterol 124mg
Sodium 157mg
Total Carbohydrate 10g
Dietary Fiber 5g
Sugars 2g
Protein 6g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.

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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
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On Low Carb Lemon Chia Seed Muffins
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November 23, 2023 - 04:29
Add a Rating:
Really tasty and moist! My one year old enjoyed it a lot! Added a little honey instead of stevia and oat milk instead of almond. Turned out great! Thanks:)
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Linda Mc
May 28, 2023 - 08:19
I’d like to add unsweetened coconut to the recipe for more texture. Would I just add with no adaptations or would i reduce coconut flour or add a little more moisture? Recipe looks great and I also might try it as a small loaf. Have you tried a loaf and what cooking time might be best. I’m also high altitude 5k if any other changes are needed.
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May 30, 2023 - 13:40
I haven't tried adding shredded coconut so I am not sure. Let us know how it turns out!
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August 17, 2022 - 04:02
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These are tasty - lovely coconutty lemony flavour, but agree with a previous reviewer - mine did not rise. They remained exactly how they were poured in. I followed the recipe exactly (swapping in the honey instead of stevia). Still lovely but not perfectly rounded, risen muffins like the picture
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Marianna Gonzalez
December 26, 2021 - 16:43
Hi my batter came out very thick. Is that normal? I was looking for a more cake style batter.
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July 13, 2021 - 05:14
Can I substitute almond flour for the coconut flour?
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January 2, 2019 - 12:15
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I made these muffins and they did not rise at all. I wanted to ask about the 2T melted coconut oil. There was no instructions on how to add it? Thanks.
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January 3, 2019 - 09:57
Thanks for the feedback - just updated it. That's strange that they didn't rise. Is there any chance you used baking powder instead of baking soda?
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April 22, 2020 - 07:33
This was the mistake I made powder instead of soda!!
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January 3, 2019 - 14:14
Thanks so much for the response and update! I definitely used baking soda so it must have been something else I did. They did turn out moist and yummy. I love your website and recipes. Happy 2019! :)
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Alice Anderson
January 31, 2017 - 14:45
Add a Rating:
These muffins turned out moist with a good texture, not very sweet. I think they could use more lemon. Maybe just add a little more lemon peel?
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