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What If “Medication vs. Natural” Is the Wrong Question?

By Dr. Marie Nowlan, ND9/21/2026
a close up of pills and pills bottles

How autoimmune care can protect your future health while supporting the life you’re living today.

There’s something that sometimes surprises people when they learn that I’m both a naturopathic doctor and someone who has lived with autoimmune disease for many years:

I’m not anti-medication.

Not even close.

I’m very evidence-informed in how I approach autoimmune disease. And the reality is that for many autoimmune conditions, disease-modifying medications can do something incredibly important: reduce disease activity and help protect tissue from ongoing damage.

That matters.

It matters even when you're eating well. Even when you're exercising. Even when you're managing stress, prioritizing sleep, taking supplements and doing all the things you're “supposed” to be doing.

And this is something I think we need to talk about more openly in the natural health world.

The pressure to do it “naturally”

There can be a strange badge of honour attached to managing chronic illness without medication.

I’ve seen it in patients. I've seen it online.

And I've felt it myself.

There's this subtle idea that if we just find the right diet, the right supplements, the right root cause, or become disciplined enough with our lifestyle, maybe we won't need medication.

And if we do?

Somehow we've failed.

What makes this particularly interesting for me is that I knew better.

I understood the evidence. I understood what my medications were designed to do. I understood that nutrition, exercise and stress management weren't interchangeable with disease-modifying treatment.

And I still had to work through that feeling.

Over time, I've replaced much of it with something very different:

Gratitude.

Gratitude that these medications exist.

Gratitude for the researchers who continue to push autoimmune treatment forward.

And gratitude that I don't have to choose between using modern medicine to help protect my body and using naturopathic medicine to support how I feel and function within that body.

Because this was never supposed to be an either/or.

Controlling disease doesn't always mean feeling well

This is where I think an important distinction gets lost in conversations about autoimmune treatment.

Medication can help change the course of disease. But that doesn't necessarily mean you feel well.

You can have less disease activity and still be exhausted.

You can have reassuring imaging or bloodwork and still struggle with brain fog.

You can be considered medically stable and still notice changes in your sleep, mood, digestion, exercise tolerance or ability to recover from stress.

In other words:

You can be medically stable and still not feel like yourself.

And that's where I believe naturopathic medicine can add so much.

We work alongside disease-modifying therapies, not around them

When someone comes to see me with an autoimmune condition, my goal isn't to find a way around appropriate medical treatment.

It's to look at the rest of the picture. (Blog: Autoimmunity Doesn’t Happen Overnight: Uncovering the Root Causes)

What factors may be contributing to fatigue?

Any nutrient deficiencies needing to be ruled out?

How are sleep and circadian rhythms affecting energy and recovery?

What is happening in the gut? Are there digestive concerns that haven't been addressed?

Is someone getting enough protein, fibre and micronutrients to support their overall health?

How is metabolic health?

How much movement can their body currently tolerate, and how do we gradually build strength and resilience without constantly pushing beyond their capacity? (BLOG: Is Exercise Good for Autoimmune Disease? Finding the Right Amount)

Are there medication side effects or longer-term risks that warrant additional support or monitoring?

And perhaps most importantly: what is getting in the way of this person living their life?

That's a very different question from simply asking whether their disease is stable.

This is the space where I think naturopathic medicine shines.

Not as an alternative to appropriate disease-modifying treatment, but as a complement to it.

Disease activity is important. So is quality of life.

When you live with autoimmune disease, your goals are rarely limited to what shows up on a scan or blood test.

You want enough energy to make it through your day.

You want to be able to think clearly.

You want to move your body and trust that you'll recover.

You want to sleep well.

You want to make plans without constantly calculating how much energy they will cost you.

You want to be present with the people you love.

You want to feel more like yourself.

Those things matter, too.

This is why I don't see conventional and naturopathic medicine as opposing sides.

For many people with autoimmune disease, medication is an important consideration. It may help reduce disease activity and protect against future damage.

Naturopathic medicine can then ask a different, complementary question:

How do we support the person living inside that diagnosis?

Taking medication doesn't mean you failed

If there's one thing I wish we could remove from conversations about autoimmune disease, it's the idea that needing medication somehow represents a failure.

You didn't fail because your diet wasn't perfect enough.

You didn't fail because you couldn't meditate your way out of inflammation.

You didn't fail because supplements weren't enough.

And choosing medication doesn't erase all the other work you're doing to support your health.

Nutrition still matters.

Movement still matters.

Sleep matters.

Stress and nervous system regulation matter.

Connection, joy, purpose and quality of life matter.

And appropriate medical treatment matters.

Sometimes taking the medication is part of taking care of yourself.

The goal doesn't have to be choosing the most “natural” path.

It can simply be choosing the tools that make sense for your individual situation, with good evidence, thoughtful care and the right support around you.

Because protecting your future health matters.

And so does supporting the life you're living right now.

Looking for a different approach to autoimmune care?

If you're living with autoimmunity and feel like there's a gap between managing your disease and actually feeling like yourself, this is the work I do.

My approach is designed to complement your existing medical care while investigating the factors that may be affecting your energy, resilience and quality of life.

Ready to explore what that could look like for you? Book a complimentary 15-minute Discovery Call.

Common Questions About Medication and Naturopathic Autoimmune Care (FAQs)

Can naturopathic medicine be used alongside autoimmune medication?

Absolutely. In fact, this is how I approach autoimmune care for many of my patients.

We work alongside disease-modifying therapies, not around them.

For many autoimmune conditions, medication can play an important role in reducing disease activity and protecting against future tissue damage. Naturopathic medicine can complement that care by looking at areas that may not be fully addressed by medication alone, including nutrition, nutrient status, sleep, digestion, metabolic health, movement, stress and nervous system regulation, and overall quality of life.

We can also consider medication side effects, nutrient interactions or depletions where relevant, and other factors that may affect how well someone tolerates and stays consistent with their treatment.

The goal isn't to choose conventional or naturopathic medicine. It's to use the appropriate tools from both to support the whole person.

Can lifestyle changes reduce the need for autoimmune medication?

Sometimes lifestyle changes can make a significant difference in symptoms, inflammatory burden, metabolic health and overall quality of life. Depending on the condition and the individual, changes in disease activity or other health factors may also affect medication decisions over time.

But this is an important distinction: needing less medication should not be the measure of whether naturopathic care has “worked.”

Medication decisions depend on the specific autoimmune disease, its activity and severity, risk of future tissue damage, response to treatment and many other individual factors. Any changes to disease-modifying medication should be made with the prescribing medical team.

Someone can be doing an incredible job supporting their health and still benefit from medication.

For me, success looks much bigger than whether someone takes a prescription. Are flares becoming less frequent or easier to recover from? Is energy improving? Are they getting stronger? Sleeping better? Thinking more clearly? Are we improving the health factors we can influence and helping them participate more fully in their life?

Those outcomes matter, too.

Why can I still have fatigue and brain fog even when my autoimmune disease is stable?

Because disease activity is only one piece of the puzzle.

Medication may be doing exactly what we want it to do by controlling disease activity or reducing the risk of future damage, while fatigue, brain fog or reduced resilience continue for other reasons.

That's where I like to investigate.

We may look at sleep and circadian rhythm, nutrient status, nutrition, blood sugar regulation, mitochondrial health, movement and muscle mass, stress physiology, hormonal health, digestion, medication effects and other factors that could be contributing to how someone feels.

Not every symptom has a simple explanation, and we don't always find one single “root cause.” Often, there are several pieces adding to the overall load.

Being medically stable doesn't mean you should simply accept feeling unwell. It means we can ask another question: what else might be influencing how you feel and function?

Do naturopathic doctors recommend stopping medication?

Naturopathic medicine should not automatically mean “getting off medication.”

My goal is never to prove that someone can manage their autoimmune disease naturally. My goal is to help them make informed decisions about their health while working collaboratively with the rest of their healthcare team.

For some people, medication may be an important part of their care long-term. For others, their medication needs may change over time. Those decisions are individualized and should be made with the clinician prescribing and monitoring the medication.

What I can do is help support the health of the person taking that medication: investigate ongoing symptoms, support quality of life, address modifiable risk factors, and help build the foundations that allow them to feel and function as well as possible.

Because ultimately, the goal isn't to earn a badge for doing it “naturally.”

It's to protect your future health while helping you actually participate in the life you're protecting.

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