A low FODMAP custard cupcake on a marble plate

Low FODMAP custard cupcakes

I wanted to make a simple cake recipe, but with just a little extra. I was thinking about those delicious custard cupcakes that you can buy at the supermarket and I thought I’m going to make a low FODMAP version of them. I present: low FODMAP custard cupcakes!

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How to make custard cupcakes?

The basis of these cakes is simple. That’s just a normal vanilla cupcake. For this I use the following ingredients:

  • Gluten-free baking mix: I always use Schär Mix It Universal. This recipe works best with this baking mix or a similar mix.
  • Granulated sugar
  • Butter: because of the processing process, butter contains almost no lactose anymore and is therefore low FODMAP.

    If you have to eat strictly lactose-free or if you already have complaints from a very small amount of lactose, you can replace the butter with lactose-free margarine.

  • Lactose-free milk: you can use lactose-free cow’s milk or a vegetable milk, such as almond milk.
  • Eggs
  • Vanilla extract
A hand holding a gluten-free custard cupcake

The custard

The custard filling for the cakes is made by making pastry cream. I was very lazy and used a package from Dr. Oetker. This pack contains powder and you only need to add water or milk to make custard

Please note that this custard is not lactose-free. So you can only use this if you tolerate lactose. I am lactose intolerant myself, but I took a lactase pill to eat this custard. 

You can of course also make the pastry cream yourself, then you can make it completely lactose-free. I recommend this recipe from Jamie Oliver.

Replace the regular milk in the recipe with lactose-free cow’s milk.

Adding the custard to the cupcakes is very simple. You can do that with a piping bag, to do it very neatly, but that is not necessary.

I just filled the cupcake liners for 2/3 with batter. Then spoon a heaping teaspoon of pastry cream in the middle of the batter. During baking you will see that the custard settles in the middle of the cake.

This way you have delicious cakes filled with custard!

Drie glutenvrije custard cakejes bij elkaar

Frequently asked questions

How long can I store the low FODMAP custard cakes?

Store the cakes in a sealed container. Then they stay tasty for 3-4 days.

Can I freeze the cakes? 

Yes, that’s possible. Then pack the cakes airtight. For example in a plastic container.

Can I also use flour type X?

For the best results, I recommend using Schär Mix It Universal or a similar flour mix for these cakes. This is a flour mix based on rice flour and potato starch.

I do not recommend flours such as almond flour and coconut flour. These are not or only to a limited extent low FODMAP. In addition, they have completely different properties. This means that you need a different recipe to make cake with such a flour.

I do not recommend buckwheat flour, because it has a very present flavour. I expect spelt flour will work for this recipe, but I haven’t tested that yet.

Will you let me know if you have made my low FODMAP custard cupcakes? I would love it if you would let me know what you think about the recipe by leaving a comment and a rating below. You can also share your creations with me by tagging me on Instagram @karlijnskitchen or by using the hashtag #karlijnskitchen. 

Three low FODMAP custard cupcakes of which one is broken in half
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Three low FODMAP custard cupcakes of which one is broken in half

Low FODMAP custard cupcakes

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  • Author: Karlijn
  • Total Time: 35 min
  • Servings: 12 1x
  • Diet: Gluten Free


Simple low FODMAP custard cupcakes! Vanilla cakes with a filling of pastry cream. Delicious with a cup of coffee. Gluten-free and low lactose.


  • 200 g (1 1/4 cup) gluten-free flour mix (I use Schär Mix It Universal)
  • 170 g (3/4 cup) butter, at room temperature
  • 170 g (3/4 cup) sugar
  • 3 eggs, at room temperature
  • 1/4 tsp vanilla extract
  • 2 tbsp lactose-free milk or almond milk
  • 1 serving of pastry cream (for example according to this recipe, where you use lactose-free milk)
  • A pinch of salt
  • 12 baking cups
  • A muffin pan


  1. Pre-heat the oven to 180 degrees Celsius (350 F).
  2. Mix the butter creamy with the sugar.
  3. Add the eggs one by one while you mix in between.
  4. Add the vanilla extract and the milk and mix well.
  5. Fold the baking mix and the salt into the mixture with a spatula.
  6. Put baking cups into a muffin tin. Fill the cups for 2/3 with batter.
  7. Add a large teaspoon of pastry cream into the middle of each baking cup.
  8. Bake the cupcakes in the oven for 25 minutes. They are done when a toothpick comes out clean. Because every oven works different, your cupcakes might need a few minutes longer or shorter. Therefore keep an eye on them at the end of the baking time.
  • Prep Time: 10 min
  • Cook Time: 25 min
  • Category: Cake
  • Method: Oven
  • Cuisine: International
5 gluten-free custard cupcakes of which one is broken in half
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  • Jenny K says:

    Have the ingredients for the Schär Mix It Universal flour changed since you posted this recipe? You describe it as “a flour mix based on rice flour and potato starch”, but the Schär website now lists maize starch as its biggest ingredient::

    “maize starch, rice flour,, sorghum flour, rice starch, dextrose, vegetable fibre (psyllium), pea protein, thickener: hydroxypropyl methyl cellulose, salt”

    In the UK we can get Doves Farm Free From Gluten plain flour (yes, there are 3 Es in the name!) which seems to be closer to what you recommend. Although it does include buckwheat, that’is the last/smallest ingredient so shouldn’t be too dominant: “Flour Blend (Rice, Potato, Tapioca, Maize, Buckwheat)”. Would that be a better choice than the new Schär version?

    • Karlijn says:

      That is definitely possible. I still use the new version of Schar Mix It Universal and that works fine. But you could definitely also use Doves Farm Freee, that is indeed a similar mix. Supermarkets in the Netherlands recently started selling it too and I use both mixes now and then 🙂

      • Jenny K says:

        Thank you! Doves is the one I have in the cupboard, and it is less than half the price of the Schar locally, so I will use that to try your baking recipes, but it is good to know that I can still use the Schar if I have any problem getting the Doves.

  • Jana says:

    I am so excited to try this recipe out! I’m wondering if i can add baking soda/powder so the muffins can rise. I’m a newbie to low fodmap diets. I don’t know if baking soda/powder are low fodmap ingredients.

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