Lyme Friendly Vegan Pumpkin Muffins

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As with our Lyme Friendly Pumpkin Pie Recipe, this recipe is designed with my Lyme community in focus. Many suffering with Lyme disease experience a wide variety of food allergies, some of which can be identified on GI map testing, others which are not so easily identified. Our sensitive group often experience gluten intolerance, dairy intolerance, egg allergies and difficulty with nightshade vegetables. 

The tough part is that most Lymies are also very sensitive to soy and almonds, so standard vegan isn’t a straightforward option either. Furthermore, when it comes to chemicals in food, no one can sniff those out more thoroughly than an individual struggling with Lyme Disease. These folks KNOW that toxins are everywhere and avoiding them in food is critical for their healing. My 10 year old son once took a small bite of a scoop of his favorite flavored and seemingly “clean” coconut milk ice cream, only to promptly spit it out and say, “nope, there’s poison in there.”  Having Lyme disease is certainly one way to become aware of the invisible danger that surrounds us all, isn’t it?

Our vegan recipe DOES contain a gluten crust recipe, which can be substituted for a gluten free crust for those who have true celiac issues. In my experience working with Lyme clients, the issue of gluten intolerance often has to do with the bromination of the flour. When flour is made ready to be stored on the shelf, bromine is added. This process keeps the flour from spoiling, but adds a toxicant/preservative and one that displaced iodine, adding to the ongoing health epidemic of thyroid dysfunction among other health issues. 

If you use a full flour, one that is milled freshly from the wheat berries, you will have a complete source of nutrition including protein, fiber, zinc, magnesium, iron and the highest source of vitamin E available. Organic wheat berries are an excellent source of pesticide and toxin-free flour. If you do suffer from true celiac, even freshly milled wheat flour should be avoided. If the issue is gluten intolerance, you will likely be very excited to discover that you can indeed enjoy bread every once and a while.

If you are just starting your journey of healing your body from the ravages of Lyme disease and you have not yet gotten the inflammation of your gut under control, then I would advocate for you to continue with gluten-free approaches and switch to the fresh milled flour once you have restored the health of your gut.

In this case the flours that I find to be the most tolerated are amaranth, barley, coconut, cassava, quinoa, using arrowroot as the binder.

Avoid chickpea, almond, rice and corn flours as well as tapioca powder. (I know, these are the more common ones on the shelves… welcome to Lyme food sensitivities.. 🙁 )

My kids loved this recipe so much that they asked for these instead of birthday cake. “Mommy, can I have these for my birthday?” I would say they were a big hit!

Fair warning: this is another MADE FROM SCRATCH type of recipe.. For those who are struggling with a lot of fatigue and can’t imagine making something from scratch, this recipe can be done in stages as you have bursts of energy. I made this recipe over the course of two days myself. I roasted the pumpkins and milled the flours one day and I  recruited the kids to scoop the pumpkins while I mixed the dry ingredients and it all came together just fine.


2 cups Fresh Milled flour or your favorite gluten free combination (250g)
1 cup Light Brown Sugar (200g)
½ cup Coconut Sugar (100g)
1 tsp Baking Soda
1 tsp Baking Powder
½ tsp Salt
2 tsp cinnamon
1 tsp ginger
¼ tsp nutmeg
½ tsp cardomom
1 ½ cups Pumpkin Purée (337g) fresh preferred (if canned use Libby’s organic brand)
1 tsp Vanilla Extract
¼ cup Coconut Oil (60ml) Melted
1 Tbs White distilled vinegar

1 Flax Egg (1 Tbsp Ground Flaxseed Meal with 3 Tbsp Hot Water)

1 cup Pecan Nuts (109g) Chopped, plus more to place directly on top of the muffins


  1. Preheat the oven to 350°F (180°C). Spray a muffin tray with non-stick spray and set aside.
  2. Sift the flour into a mixing bowl and add the brown and white sugar, baking soda, baking powder, salt and pumpkin pie spice.
  3. Prepare your flax egg by adding 1 Tbsp of ground flaxseed meal to a bowl and then pouring in 3 Tbsp of hot water and allowing to sit for a minute to become gloopy.
  4. Add the pumpkin purée, vanilla, melted coconut oil and apple cider vinegar to the mixing bowl.
  5. Add your flax egg.
  6. Mix together with a spoon until well combined. The batter will be thick.
  7. Lastly, add the pecan nuts and stir in.
  8. Divide the batter evenly amongst the muffin partitions in your prepared muffin tray. Add a few more chopped pecans directly to the top of the muffins.
  9. Bake in the oven for 20-25 minutes or until a toothpick inserted into the center of one of the muffins comes out clean.
  10. Allow the muffins to cool for a few minutes and then transfer them to a wire cooling rack to cool completely.



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