Recipe

Easy Baked Chicken Flautas

Published on Friday, January 16, 2026
by Jessie Hulsey

Health & Wellness

Low FODMAP Chicken Flautas: Crispy, Gut-Friendly Comfort Food

Flautas are one of those foods that feel fun and comforting at the same time. Crispy on the outside, warm and savory on the inside, they’re often a go-to at restaurants or taco nights at home. The challenge is that traditional flautas usually include ingredients like onion-heavy fillings, wheat tortillas, or spicy sauces that don’t always sit well with sensitive digestion.

This Low FODMAP Chicken Flautas recipe keeps all the crunch and flavor you expect, while using simple, gut-friendly ingredients. With shredded chicken, Low FODMAP salsa, melty cheese, and gluten-free flour tortillas, these flautas are approachable, family-friendly, and perfect for an easy dinner or fun appetizer night.

What Makes These Flautas Low FODMAP?

A few ingredient choices make all the difference here.

Shredded chicken: Plain cooked chicken is naturally Low FODMAP and provides protein without added triggers. Using rotisserie-style chicken works well, as long as it’s simply seasoned and free of garlic or onion powders.
Low FODMAP salsa: Many salsas contain onion or garlic, but there are certified Low FODMAP options that still bring brightness and flavor without upsetting digestion.
Cheese: Shredded cheddar, Monterey Jack, or a Mexican-style blend are all Low FODMAP in appropriate portions and help bind the filling while adding richness.
Gluten-free flour tortillas: These replace traditional wheat tortillas and roll up beautifully for flautas, creating that signature crisp texture once cooked.

Substitutions & Variations

This recipe is easy to customize while staying Low FODMAP-friendly!

Shredded turkey works well if you have leftovers on hand, or you can use ground chicken or beef cooked with mild seasoning.
Lactose-free cheese is a great option if you’re especially sensitive to lactose.
Make them extra crispy by brushing or spraying the tortillas lightly with oil before cooking for a deeper golden finish.
Finely diced red bell peppers or chopped green onion tops can be mixed into the filling for added color and texture without increasing FODMAP load.

Tips for the Best Low FODMAP Flautas

These quick tips help you get flautas that are crispy, golden, and easy to roll every time.

Gently warming gluten-free tortillas makes them more pliable and prevents cracking when rolling.
Don’t overfill! A modest amount of filling helps the flautas roll tightly and crisp evenly.
Placing the flautas seam-side down helps them stay rolled and crisp properly during cooking.
Overcooking can dry them out, especially with gluten-free tortillas, so make sure to cook just until golden!

Serving Ideas

Flautas are fun to customize, and the right toppings can turn them into a complete meal.

Fresh pico de gallo made without onion
Creamy guacamole in a Low FODMAP portion
Lactose-free sour cream or plain Greek yogurt
A taco side salad with cilantro vinaigrette
Cilantro-lime rice or seasoned white rice

FAQs

Can I make these flautas ahead of time?

Yes. You can assemble them a few hours ahead and store them covered in the refrigerator. Cook just before serving for the best texture.

Are flautas and taquitos the same thing?

They’re very similar. Flautas are typically made with larger tortillas and rolled thinner, while taquitos are usually smaller, but the preparation is quite similar.

Can I freeze Low FODMAP flautas?

Yes, you can freeze assembled but uncooked flautas in a single layer, then transfer them to a freezer-safe bag and cook straight from frozen, adding a few extra minutes to the cook time.

Ingredients

Instructions

Ingredients

3 cups shredded cooked chicken
½ cup Low FODMAP salsa
1 cup shredded cheese (cheddar, Monterey Jack, or lactose-free)
20 gluten-free flour tortillas (soft taco size)
1 tablespoon oil (olive or avocado, for brushing or spraying)
Optional toppings: pico de gallo (without onion), guacamole, lactose-free sour cream or plain Greek yogurt, chopped cilantro, lime wedges

Instructions

Preheat the oven to 425°F and line a baking sheet with parchment paper.
In a medium bowl, stir together the shredded chicken, salsa, and cheese until evenly combined.
Warm the tortillas in the microwave briefly so they’re pliable, then place about ¼ cup of filling along one edge of each tortilla.
Roll the tortillas tightly and place them seam-side down on the prepared baking sheet.
Lightly brush or spray the flautas with oil to help them crisp in the oven.
Bake for 15–20 minutes, flipping halfway through, until golden brown and crisp.
Remove from the oven and let cool slightly before serving with your favorite Low FODMAP toppings.

Nutrition Facts

Serving Size: 12 servings

Servings Per Recipe: 12

Amount Per Serving Calories 254 % Daily Value* Total Fat 7.7g 11% Saturated Fat 1.9g 9% Trans Fat 0.0g Sodium 665.0mg 27% Total Carbohydrate 27.0g 9% Dietary Fiber 0.0g 0% Sugars 2.0g Protein 15.9g

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