Healthy Apple Cranberry Muffins (Vegan & Gluten-Free)

Simple and delicious, these healthy Apple Cranberry Muffins are perfect for breakfast on-the-go and sweet enough to enjoy as a dessert.  

Packed with nutrients, these oat-based muffins are friendly for many dietary restrictions. They are:

  • Gluten-Free
  • Dairy-Free
  • Soy-Free
  • Egg-Free
  • Nightshade-Free
  • Vegan and Vegetarian 
  • Kosher

Nutritional Benefits at a Glance for IBD:

Unsweetened Almond Milk:

Almond milk can be a great dairy-free alternative for those who are lactose intolerant or following a lactose-free diet.

We used unsweetened almond milk in this recipe, as concentrated amounts of sugar found in sweetened beverages may worsen diarrhea. Here are a few of our favorite brands of unsweetened almond milk (please note that we are not paid or sponsored to mention these brands):

  • Simply Almond Milk, Unsweetened Original
  • Elmhurst Milked Almonds, Unsweetened
  • Malk, Unsweetened Almond Malk

For those who are trying to increase calcium and vitamin B12 intake, using fortified almond milk is an excellent way to do so.

Coconut Sugar:

This natural sweetener has become increasingly popular, especially among people with diabetes, as it is considered to be more nutritious and lower on the glycemic index than cane sugar.  

Coconut sugar contains trace amounts of iron, zinc, calcium, and potassium, unlike its counterpart, table sugar. However, it is important to note that these minerals are found in such small amounts and do not contribute to a significant health benefit. 

Oat Flour :

Oat flour is a nutritious whole grain flour that can be store bought or easily made at home. With a nutty flavor and a tender crumb, oat flour is the perfect gluten-free alternative for muffins.

Oat flour is a great choice for IBD warriors as it contains anti-inflammatory antioxidants and is packed with gut-friendly soluble fiber. Additionally, oat flour is loaded with several nutrients including zinc, calcium, magnesium, iron, thiamin, and phosphorus. 

Finally, these muffins contain 4 grams of protein per serving, which primarily comes from the oat flour in this recipe. This makes oat flour a great choice for those trying to increase protein intake, which is particularly important for those experiencing high levels of inflammation and/or taking corticosteroids. 

Ground Flax Seed:

Ground flax seed is a good source of plant-based omega-3’s, an anti-inflammatory nutrient that may help to reduce IBD disease activity and increase time in remission.  

Ground flax seed is recommended over whole flaxseed because the ground form is easier to digest. Whole flaxseed may pass through the intestine undigested, which means you won’t get all of the nutritional benefits! Additionally, ground flax may be easier to tolerate by people with IBD.

Unsweetened Cranberries:

Dried cranberries are a good source of Vitamin C, which acts as an antioxidant, and is important in wound healing. This is particularly important during a Crohns or Colitis flare up. Cranberries are also a good source of Vitamin E, Vitamin K, and manganese. 

We used unsweetened cranberries to reduce the overall sugar content of the recipe.


Apples contain a variety of vitamins, minerals, and antioxidants. During a flare, the insoluble fiber-rich skin of apples can be harsh on the digestive system.  However, once the skin is removed, the remaining soluble fiber called “pectin” gently aids in digestion by firming up loose bowel movements, making apples a great choice for IBD warriors.  

What’s the Secret to Making a Moist Muffin?

There are three secrets to baking moist muffins:

  • Don’t overmix the batter.
  • Add a pureed or grated fruit in addition to the oil
  • Be careful not to overbake. 

How to Make Apple Cranberry Muffins: The Simplest, Easiest Method

Preheat the oven and prepare a standard 12-well muffin tin with muffin liners. Mix the dry ingredients together in a large bowl; set aside. Mix the wet ingredients in a medium bowl until well combined. Fold the wet ingredients into the dry. Fold in any mix-ins (in this case, grated apple and cranberries). Divide the mixture among prepared muffin tin wells and bake!

Can I Make Mini Apple Cranberry Muffins?

Yes, this recipe will make about 24 mini muffins. Bake at 350 degrees Fahrenheit for 12 minutes.  

How to Store Muffins:

Allow muffins to cool completely before storing them in an airtight container. Store at room temperature for 3-4 days or in the refrigerator for up to one week.  

Can You Freeze Muffins?

These Apple Cranberry Muffins are perfect to freeze for later. Just place them in an airtight container or a gallon-size plastic bag. Remove as much air as possible and freeze for up to 3 months.  

An up-close image of apple cranberry muffins on a granite countertop surrounded by cranberries

Healthy Apple Cranberry Muffins

Robin Phipps and Danielle Gaffen, MS, RDN, LD; Photo courtesy of Robin Phipps
Simple and delicious, these healthy Apple Cranberry Muffins are perfect for breakfast on-the-go and sweet enough to enjoy as a dessert.
Total Time 35 minutes
Course Breakfast, Dessert
Cuisine American
Servings 12
Calories 181 kcal


  • 1 Bowl Small
  • 1 Bowl Large
  • 1 Mixing Spoon
  • 1 Muffin Tray
  • Muffin Tray Liners


  • 2 tbsp Ground Flax Seed
  • 1/4 cup Water
  • 2 cups Oat Flour
  • 1/3 cup Coconut Sugar
  • 1 tsp Baking Soda
  • 1/2 tsp Sea Salt
  • 1 tsp Cinnamon
  • 2/3 cup Unsweetened almond milk
  • 2 Apples small, peeled, grated
  • 1/4 cup Coconut Oil melted
  • 3/4 cup Dried Unsweetened Cranberries


  • Preheat the oven to 350ºF (177ºC) and line a muffin tray with liners or use a silicone muffin tray.
  • In a small bowl, mix the ground flax with water and set aside.
  • In a large mixing bowl, add the oat flour, coconut sugar, baking soda, sea salt and cinnamon. Whisk well. Then add the ground flax/water mix, almond milk, grated apple and melted coconut oil. Mix well to combine using a spoon or spatula. Gently fold in the dried cranberries.
  • Divide the batter into the prepared muffin tray. Bake for 22 to 24 minutes.
  • Remove the muffins from the oven and let them cool before placing them on a cooling rack for 15 minutes. Serve and enjoy!


Serving Size:
One serving is equal to one small muffin. 
These muffins are quite dense due to the oat flour. They do not rise very much.  
Nut Free:  
Make this recipe nut-free by using coconut, hemp, or rice milk in place of almond milk.
Optional toppings:
 Top these muffins with your favorite nut butter for added protein.  
No Coconut Oil:
Try this recipe with butter or ghee instead. 
No Ground Flax Seed:
Flax “eggs” are prepared by mixing ground flaxseed with water. They have become a  popular egg substitute among vegan and others with egg allergies or sensitivities.  However, this recipe can also be prepared with two large eggs in place of the flax “egg”  if eggs are tolerated.  


Serving: 1muffinCalories: 181kcalCarbohydrates: 27gProtein: 4gFat: 7gSaturated Fat: 4gSodium: 212mgPotassium: 35mgFiber: 4gSugar: 12gVitamin A: 43IUCalcium: 40mg
Keyword dairy-free, egg-free, gluten-free, kosher, nightshade-free, soy-free, vegan, vegetarian


About the Author

Picture of Danielle Gaffen, MS, RDN, LD

Danielle Gaffen, MS, RDN, LD

Understanding the link between nutrition and gut disease prompted me to obtain my master’s degree in Nutritional Sciences at San Diego State University and become an IBD Registered Dietitian Nutritionist. Now I work with people who have Crohn’s and colitis who are struggling with confusion around what to eat. My favorite part is helping them to build confidence to eat without fear while managing their symptoms.

Explore more recipes

Food Survival Guide During an IBD Flare

Learn 9 key food tips from IBD dietitian Danielle Gaffen to help get you through a flare and reduce symptoms.

By completing this form you also agree to receive our IBD newsletter. Unsubscribe at any time.