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Vegan Lemon Poppy Seed Muffins

Name: Vegan Lemon Poppy Seed Muffins
Prep time: 10 min
Cook time: 25 min
Total time: 35 min
Ingredients: 2 cups oat flour (, gluten free if needed ); ¾ cup fine grain almond flour; 1 ¼ cup cane sugar (, see note ); 1 tablespoon baking powder; ½ teaspoon sea salt; ¾ cup light coconut milk; ¾ cup lemon juice; ½ cup unsweetened apple sauce; 1 tablespoon vanilla extract; ¼ cup poppyseeds; 2 tablespoons lemon zest; ½ cup powdered sugar; 1 tablespoon lemon juice

By Sophia DeSantis, Reviewed by Anjali Shah on August 11, 2025

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These Vegan Lemon Poppy Seed Muffins are bright, zesty, and incredibly moist. I make them with fresh lemon, poppy seeds, and a mixture of oat and almond flour for a delicious gluten-free treat. Ready in just 35 minutes, they’re perfect for sharing at kids’ parties or afternoon snacks!

A group of lemon poppy seed muffins in front of lemons and one with a bite out of it in the front.

My love for lemony baked goods started with this sublime gluten-free vegan lemon tart I created a few years ago, which quickly became a family favorite. The bright citrus flavor and nutty oat base worked so well that it gave me the inspiration to make this lemon muffin recipe.

Table of Contents hide

👩🏽‍🍳 Why I Love This Recipe

🍽 Serving Suggestions

🧊 Storage Directions

❓Recipe FAQs

🧇 More Healthy Muffins Recipes!

📋 Recipe Card

These are so easy to make, and I have to say adding coconut milk and apple sauce was my best move because they stay moist for days. My boys love them so much that they now grab a muffin for breakfast instead of asking for vegan lemon pancakes and honestly, I’m not mad about it. 🙂

👩🏽‍🍳 Why I Love This Recipe

My health-conscious outlook on food has led me to create so many treats that are both delicious and packed with goodness. These vegan lemon muffins are exactly that! The combination of oat and almond flour creates the perfect gluten-free tender crumb, while fresh lemon juice and zest bring such bright, natural flavor that keeps them moist and juicy, along with the coconut milk and apple sauce. I always sneak a few extra muffins into their lunchboxes to share with their friends at school!

The recipe is similar to cookies and sweet bread, where it’s basically a dump-and-stir method. Separating the dry and wet ingredients and then slowly introducing them like shy friends. The optional lemon icing glaze makes them extra delicious but honestly, they’re perfectly delicious without it too.

My vegan muffins have become my go-to healthy sweet treat for everything from breakfast to school snacks to after-school playdates, and they’re naturally vegan and gluten-free, making them perfect for when I need to accommodate different dietary needs. Last month, I brought them to my son’s class fundraiser, and one mom texted me later asking for the recipe because her son has a gluten allergy, she couldn’t believe they were both vegan and gluten-free!

🥘 Ingredients

Here’s what I grab when I’m making my Vegan Lemon Poppy Seed Muffins. I keep most of these ingredients stocked in my pantry, so it’s easy to make a batch whenever the craving hits.

Flours: I use oat flour and almond flour so the muffins stay soft and tender. If I have gluten free oat flour, I make sure to use that.

Sweetener and flavor: I add cane sugar, vanilla, and plenty of fresh lemon juice and zest for the best flavor.

Leavening and seasoning: A bit of baking powder and sea salt help them rise and taste great.

Moisture: Light coconut milk and apple sauce keep the muffins soft for days.

Texture: Poppy seeds give a little crunch the kids and I love.

Optional glaze: I mix powdered sugar with lemon juice for a sweet topping that adds extra lemon flavor.

🔪 How To Make

You’re going to love this vegan muffin recipe, it’s one I make all the time. It only takes about 10 minutes to mix everything together and around 30 minutes in the oven for a sweet fresh batch.

Mix the ingredients: I add all the dry ingredients, except for the poppy seeds, to a large bowl and whisk them together until everything is well combined.

A whisk mixing flours in a glass bowl sitting on a yellow surface.

Mix the wet ingredients: I pour in the coconut milk, lemon juice, and apple sauce, then whisk until the batter is smooth and everything is fully blended.

A whisk in a glass bowl filled with tan colored batter on a yellow surface.

Add the extras: I gently fold in the lemon zest and poppy seeds until they are evenly mixed through the batter.

Top view of a glass bowl with batter topped with lemon zest and poppyseeds.

Prepare for baking: I spoon the batter into the muffin tins lined with baking cups, filling each one evenly.

Top view of lemon poppy seed muffin batter in a muffin tin sitting on a yellow surface.

Bake and cool: I bake the muffins until a toothpick comes out clean, then let them cool before serving.

Top view of baked lemon poppy seed muffins in a muffin tin on a yellow surface.

Make the icing: I combine the powdered sugar and lemon juice in a glass and stir until smooth.

A group of lemon poppy seed muffins without glaze surrounding a glass jar with white glaze in it.

Finish and serve: I drizzle the icing over the cooled muffins if I’m using it, then serve them right away.

A glass jar of white glaze next to lemon poppy seed muffins that have just been glazed.

💭 Expert Tips

My #1 Secret Tip for making my Vegan Lemon Poppy Seed Muffins is to check them a little early so they do not dry out. I usually peek in at about the 20 minute mark and test one with a toothpick. If it comes out clean, they are ready to come out of the oven. Every oven bakes a little differently, and I have learned the hard way that leaving them in too long can take away that soft tender texture my kids love. I would much rather have them slightly underbaked and let them finish setting as they cool than risk overbaking.

Other Tips To Keep In Mind:

Use fresh lemon juice and zest: Fresh lemons give the best flavor and aroma, so I always zest before juicing.
Measure the flour correctly: I spoon the flour into the measuring cup and level it off instead of scooping, which keeps the muffins light.
Room temperature ingredients: I let the coconut milk and apple sauce sit out for a few minutes so they mix more smoothly into the batter.
Cool completely before icing: If the muffins are even a little warm, the icing will melt right off.
Store properly: I keep them in an airtight container so they stay fresh for days, or freeze extras to enjoy later

📖 Variations

Here are three variations I love making with my Vegan Lemon Poppy Seed Muffins. You should definitely give them a try:

Blueberry Lemon: I mix in about a cup of fresh blueberries and watch them dot each muffin with little purple spots. My boys love guessing which one has the most berries, and it always turns into a playful breakfast competition.

Raspberry Almond: I swap the poppy seeds for sliced almonds and add fresh raspberries, which make them look so pretty. My husband always grabs one of these for his coffee break and says it tastes like something from a bakery.

Coconut Twist: I stir in shredded coconut for a light, tropical taste that reminds me of summer. These are the ones I like to make when we have friends over because they’re just different enough to get everyone talking.

🍽 Serving Suggestions

These bright and zesty lemon poppyseed muffins are perfect any time of day. Here are some of the ways I love to enjoy my delicious muffins:

Shakes/smoothies: Personally, I can’t think of a better way to enjoy a delicious muffin than with a smoothie or shake. I usually go for the healthy protein coffee smoothie for a boost of caffeine to complement the fresh kick of lemon. My husband, on the other hand, chooses the fancy iced ube latte for a colorful way to start his day. Ha!

Yogurt: On weekends, we often enjoy these muffins as part of our morning breakfast or brunch with some homemade vegan yogurt with fresh berries and honey. Or I make my son’s favorite Greek yogurt bowl with peanut butter. They love peanut butter, and the combination of oats and yogurt is a great match for my zesty lemon muffins. The options are endless with these vegan muffins!

🧊 Storage Directions

Refrigeration: I let the muffins cool completely, then store them in an airtight container in the fridge for up to five days.

Freezing: I place the cooled muffins in a freezer safe container or bag and freeze them for up to three months.

Reheating: I warm them in the oven at 350°F for about 5 to 7 minutes or just long enough to take the chill off.

❓Recipe FAQs

How can I make these less sweet?

If I want them a little less sweet, I just use a bit less sugar, like only 1 cup. They still rise and bake perfectly, and the lemon gives them a fresh taste even with less sugar. Sometimes I do this if I know we will be eating them for breakfast instead of dessert.

Can I use bottled lemon juice?

I always like to use fresh lemon juice because it tastes brighter and has more flavor, but bottled will work if that is what I have. I make sure it is 100 percent lemon juice with no extra sweeteners or flavors. It is a good backup when I do not have fresh lemons in the fruit bowl.

Can I bake these as mini muffins?

Yes, I bake them in a mini muffin tin for around 12 minutes and keep a close eye on them. They are perfect for lunchboxes, snack time, or when we have friends over and I want something easy to share. The smaller size also means the kids can grab two without me worrying they are eating too much at once.

A hand grabbing a lemon poppy seed muffin that has a bite out of it next to other muffins.

🧇 More Healthy Muffins Recipes!

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