RISE & RUN is an instant NY TIMES BESTSELLER! Now available anywhere books are sold. RISE & RUN is an instant NY TIMES BESTSELLER! Now available anywhere books are sold.


An Ode to Superhero Muffins

An Ode to Superhero Muffins

By Natalie Bickford, MS

Master Your Superhero Muffin Baking Skills

Superhero Muffins have taken the running community by storm. Over the last 8 years they've fueled our every adventure (and many marathons!) so they hold a special place in our hearts. You guys went crazy for the original recipe in Run Fast. Eat Slow which launched in 2016. Three cookbooks later, we now have a total of 28 Superhero Muffin recipes to satisfy every craving and a variety of dietary needs. For our latest cookbook, Rise & Run, we developed 24 all new savory and sweet variations, specially designed for busy superheroes like you!

To celebrate, we wanted to dedicate a whole blog to our beloved Superhero Muffins to give you all the tips and tricks. Learn how easy it is to take shortcuts, make substitutions, and ensure that your muffins turn out perfect every time. Plus we created Superhero Muffin superlatives (yearbook style!) to showcase all of their cute little personalities! 

Pro Muffin Tips

Best muffin tins and muffin cups.

USA pan (12-cup standard tin and 24-cup mini muffin tin) - this muffin tin has a quick-release coating for easy muffin removal and clean-up. 

If You Care parchment baking cups - the best unbleached nontoxic, nonstick, environmentally-friendly muffin cups.

Reuse-able Silicone Muffin Cups - these are genius but be warned, Elyse's kids love to play with them and it's hard to keep the full set together! 

One bowl mixing method.

Instead of mixing the dry and wet ingredients in separate bowls, save time and whisk the wet ingredients together in a large bowl, then add in the dry ingredients and stir well to combine.

Food processor.

Since our muffins sneak in grated veggies and/or grated apple, food processors save a ton of time, especially if you’re making a double batch...

Pro tip: while you're at it shred extra veggies to add to salads and bowls! Elyse loves to grate extra carrots for salads, bolognese and Sunrise Overnight Oats (page 139 in Rise & Run). 

Double batch. 

Make a double batch! That means you’ll have enough for this week and a stash in the freezer for next week (or emergencies)! Elyse grabs a muffin from the freezer for a light breakfast before every single morning run since they're easy to digest and balanced for energy. 

Storage Tips.

- Savory muffins: store in an airtight container in the fridge for up to 5 days or freeze for up to 3 months.

- Sweet muffins: store in an airtight container in the fridge for up to 7 days or freeze for up to 3 months.

We love this storage container


From the fridge: in the oven at 300F for 10 minutes or microwave on low power for 30 seconds.

From the freezer: microwave on low power for 1 minute. Or thaw overnight in the fridge.


Superhero Muffins make the most perfect travel snack. We like to pack the sweet variations for traveling since the savory muffins are a lot more perishable when unrefrigerated. Pack them in hard-sided container so they don't get smashed in your bag. Shalane and Elyse brought the Dark Chocolate Banana Superhero Muffins (page 90 in Rise & Run) and Yam Spice Superhero Muffins (page 103 in Rise & Run) to NYC to top off their tanks in the days leading up to the marathon (they both ran super fast!).  

Use ripe bananas! 

We mean it when we say “ripe” for the Dark Chocolate Banana Muffins and Superhero Smash Muffins. Your bananas need to be left out until they are brown-speckled, which can take up to two weeks (plan ahead!). They help naturally sweeten the muffins and are super mashable.

How to make substitutions 

  • Almond flour: substitute with a homemade seed meal to make nut-free or with all-purpose or whole wheat flour. If substituting with AP or whole wheat, you need to increase the fat (⅓ cup oil → ½ cup oil or 4 tbsp butter → 6 tbsp butter). Elyse loves to make fresh pumpkin seed flour in her food processor as a substitute for almond flour. 
  • Oats: we use a lot of rolled oats because it's nutrient-dense and appeals to most even those avoiding gluten. Oats are inexpensive and can be easily ground into a fresh flour in your blender. Look for certified gluten-free oats if you have an allergy. You can substitute unsweetened shredded coconut for the rolled oats in most muffin recipes, this is an easy way to make our fave Yam Spice Superhero Muffins completely grain-free. 
  • Alternative flours: for most of our muffins you can interchange the flours. Substitute oat flour, AP flour, whole wheat flour, cup-for-cup GF flour, and spelt flour in a 1:1 ratio. You can also replace any of the above flours with buckwheat flour, replacing it by no more than 1/2 cup. 
  • Grain-free: use more almond or pumpkin seed flour for the oat flour or try our Grain-Free Pineapple Coconut Muffins (page 92 in Rise & Run). Don't try to replace almond flour or oat flour with coconut flour, coconut flour has a very dry and dense composition. See tip above under Oats. 
  • Sweeteners: you can substitute 1:1 honey and maple syrup.
  • Fat: you can substitute virgin coconut oil for butter, use slightly less since coconut oil has a higher fat content.
  • Veggies: mix up the veggies! You can easily sub grated carrot for sweet potato (or any grated veggie) or fresh herbs for kale (savory muffins). 
  • Cheese: if you prefer to leave it out, add an extra 1/4 teaspoon salt. 
  • Eggs: see below
  • Yogurt: see below

Check out our favorite Rise & Run recipes (muffins included!)

How-to make your Superhero Muffin vegan. 

Most of the sweet superhero muffins can be made vegan by substituting 3 tablespoons of ground flax combined with ½ cup water for the eggs (let sit for 5 minutes). When substituting with butter, replace with equal parts coconut oil (or slightly less coconut oil). 

You can also substitute with an egg replacer. We’ve heard good things about the Bob’s Red Mill Egg Replacer.

For recipes that call for yogurt, substitute with any plain vegan yogurt alternative. 

The Savory Superhero Muffins that can be made vegan with an egg replacer are the Everything Bagel, Apple Cheddar (sub vegan cheese) and Zucchini Cornbread (sub vegan cheese). 

The Vegan Red Velvet Superhero Muffins are getting rave reviews so check out that recipe on page 106 in Rise & Run. 

Superhero Muffin Superlatives

R&R = Rise & Run
RFCFES = Run Fast. Cook Fast. Eat Slow. 
RFES = Run Fast. Eat Slow

Best Muffin for Race Day: 

Race Day Superhero Muffins (R&R, p. 110)

Runner up: Yam Spice Superhero Muffins (R&R, p. 103)

Best Muffin for the Holidays: 

Pumpkin Streusel Superhero Muffins (R&R, p. 96)

Runner up: Dark Chocolate Banana Superhero Muffins (R&R, p. 90)

Best Muffin for Fall/Winter:

Yam Spice Superhero Muffins (R&R, p. 103)

Runner up: Apple Cheddar Superhero Muffins (R&R, p. 81)

Best Muffin for Spring/Summer:

Pesto Zucchini Superhero Muffins (R&R, p. 75)

Runner up: Strawberry Rhubarb Superhero Muffins (R&R, p. 95)

Best Muffin for Kids:

Original Superhero Muffin 2.0 (R&R, p. 89) 

For Babies: Superhero Smash Muffins (R&R, p. 100)

Runner up: Lily’s Chocolate Superhero Muffins (R&R, p. 104)

Best Muffin for Iron: 

Green Eggs and Hammer On Superhero Muffins (R&R, p. 78)

Runner up: Blueberry Beet Molasses Superhero Muffins (RFCFES, p. XX)

Best Muffin for Recovery:

Quinoa Veggie Superhero Muffins (R&R, p. 84)

Runner up: Sweet Potato Kale Superhero Muffins (R&R, p. 72)

Best Muffin for Postpartum or Nursing Moms:

Lemon Chia Seed Blueberry Superhero Muffins (R&R, p. 91)

Runner up: Vegan Red Velvet Superhero Muffins (R&R, p. 106)

Best Muffin for Dessert:

Dark Chocolate Banana Superhero Muffins (R&R, p. 90)

Runner up: Pumpkin Streusel Superhero Muffins (R&R, p. 96)

Best Muffin for a Quickie: 

Mocha Madness and Coconut Vanilla Minute Mug Cakes (RFCFES, p. 214)

Runner up: Minute-Mug Lime Raspberry Superhero Muffins (R&R, p. 107)

Best Muffin for Impressing Your Date:

Everything Bagel Superhero Muffins (R&R, p.77) - recipe here

Runner up: Bacon Black Bean Superhero Muffins (R&R, p. 74)


Natalie is a nutritionist and personal chef in Bend, OR who specializes in women's health and sports nutrition. She loves creating simple, nourishing meals and recipes to fuel your life. Join Natalie's Cooking Club for weekly menus, grocery lists, videos, and meal prep tips!

Follow @elysekopecky

Follow @ShalaneFlanagan