Training Through an Autoimmune Flare: What to Do When Your Body Says Not Today

Women's Health Truth Month  ·  Week 3

Training Through
an Autoimmune Flare

What to do when your body says "not today" and why there's always a plan, no matter what kind of day it is.


Evidence-Based · Autoimmune · October 2026

You had a plan. You were consistent. You were finally feeling stronger, maybe for the first time in years. And then a flare hits. Your joints are angry. The fatigue is bone-deep. Getting off the couch feels like a workout in itself. And then the guilt shows up: I was doing so well. Now I'm starting over. Again.

I want to tell you the truth about this. Because I think a lot of women with autoimmune conditions have been handed two bad options: push through and pay for it, or stop completely and lose everything you built. There is a third option. It's the one I teach, and it's built into the way I coach.

The contextYou Are Not Alone in This

Autoimmune conditions overwhelmingly affect women. Rheumatoid arthritis, lupus, Hashimoto's, MS, psoriatic arthritis, Sjogren's. The list is long, and so is the list of women quietly managing one while trying to stay strong, stay active, and stay in their own lives.

78% Of people with autoimmune disease are women
8% Of the population lives with an autoimmune condition
80+ Known autoimmune diseases, most with no cure — only management

If you've ever felt like the fitness world doesn't know what to do with you, you're not imagining it. Most programs assume you'll feel roughly the same every day. Your body doesn't work that way. A program that doesn't account for that isn't designed for you.

That's not a reason to give up on training. It's a reason to train differently.

The evidenceStrength Training Is Not the Enemy

For a long time, the advice for women with inflammatory conditions was basically: take it easy. Rest. Don't stress the joints. The research has moved on from that.

RCT — Rheumatoid Arthritis High-intensity strength training: 119% improvement in training strength
Safe and effective for RA

People with established, controlled rheumatoid arthritis did high-intensity progressive strength training twice a week for 24 weeks. They gained lean muscle. They improved training strength by 119%. Chair stand performance improved by 30%. Walking speed improved. The researchers' conclusion was that this kind of training was safe, effective, and should be part of how RA is managed.

Not "cleared for light movement." Not "okay to try gentle stretching." High-intensity progressive strength training. Safe and effective.

EULAR Systematic Review, 2023 Exercise reduces fatigue in RA, lupus, and spondyloarthritis
Fatigue reduced across multiple conditions

A large review informing the European Alliance of Associations for Rheumatology (EULAR) guidelines looked at dozens of randomized trials on fatigue in inflammatory rheumatic diseases. Physical activity and exercise reduced fatigue in rheumatoid arthritis, lupus, and spondyloarthritis. It was rated safe.

Fatigue is one of the most debilitating and least-addressed symptoms of autoimmune disease. Finding that exercise, done with appropriate structure, actually reduces it rather than worsening it is significant. It changes the calculus entirely.

The question isn't whether to train with an autoimmune condition. It's how to train when your body is having a hard day.

The mindset shiftFlares Change the Plan, Not the Goal

A flare is not a failure. It is not a reason to quit. It is information. Your body is telling you that today needs a different dose.

The goal stays the same: build and keep muscle, protect your bones and joints, maintain the capacity to do the things you love. The plan on any given day flexes to meet you where you are. That flexibility isn't lowering the bar. It's the whole point.

Consistency, for someone with an autoimmune condition, doesn't look like showing up the same way every single day. It looks like never letting a hard day erase the habit you've built. Those are two very different things, and only one of them is actually achievable.

The systemGreen, Yellow, Red: A Framework for Every Day

This is what I use with my clients who live with autoimmune conditions, and it's built right into my virtual training. Every day, you check in with your body and pick your light. Then you have a plan that fits.

The Daily Check-In System

Green Light: Train with intent.

Energy is decent, joints feel okay, sleep was reasonable. You feel like yourself. Train your normal program. Lift with intent. Progress when you can. This is where strength is built. These are the days you show up fully and let the training do its work.


Yellow Light: Keep the engine running.

You're not great, but you're functional. Maybe you're stiff, a little achy, running on low sleep, or feeling the start of something. Lower the weight. Cut a set or two. Slow things down. Choose movements that feel okay on your joints today. You still get the win of showing up for yourself, and you protect the habit without wrecking your body.


Red Light: Rest is part of the plan.

You're in a flare. The pain, fatigue, or swelling is real today. Your plan might be gentle mobility, a few supported sit-to-stands from a chair, a short walk around the block, or simply resting and breathing. A red-light day is not falling off the program. It is the program, adapted for what your body actually needs. You rest on purpose, not because you gave up.

The magic isn't in any single workout. It's in having a plan for every kind of day. A flare doesn't erase the habit when the habit has a red-light version. Consistency over the long haul looks different for you, and it still counts. It counts a lot.

In practiceA Few Things Worth Remembering

  • Your rheumatologist or doctor is on your team. Strength training works alongside your medical care, not instead of it. If something feels new or wrong, or your flares are changing in frequency or severity, call them. You don't have to manage this alone.
  • Track your patterns. Notice what tends to come before a flare: poor sleep, high stress, a particularly full week, changes in diet or medication. That is data. Data is power. The more you understand your triggers, the better you can plan around them rather than being blindsided by them.
  • Fuel your body through it. Protein matters here too. Anti-inflammatory eating is a real thing and worth exploring with your doctor or a dietitian. On rough days, keep it simple. A protein shake, some Greek yogurt, eggs. Something is better than nothing.
  • Give yourself credit for yellow-light days. Doing a scaled workout when you feel off is still doing the hard thing. It is arguably harder than training on a good day, because you had to choose it. That choice is the habit. That habit is what builds the life.
  • Progress is not always linear, and that's okay. Two steps forward, one step back is still forward. Zoom out and you'll see how far you've come.
On comparing yourself to others

Your training timeline is yours. The woman next to you in class may not have the same variables. She's not managing what you're managing, and her progress is not the standard yours should be measured against. Your standard is your own capacity, honestly assessed on any given day, and built patiently over time. That's the only comparison that matters.

The bottom lineYou Get to Keep Going

Living with an autoimmune condition means your body needs more listening, more flexibility, and more grace than most programs give it. That is not a limitation. It is a different skill set, and it is one you are already building just by being here.

You are absolutely still allowed to get strong. You are allowed to lift heavy on your green days, scale back on your yellow days, and rest without guilt on your red days. None of those days are failures. All of them are the plan.

The women I've watched do this over time are some of the most impressive people I know. Not because it's easy for them. Because it isn't, and they do it anyway, on their terms, in a way that fits their actual life. That's what strength looks like.

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Green, yellow, and red light workout options built into every single day, so you always have a plan that fits how your body actually feels.
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You're doing the hard thing right now. Just by reading this, just by looking for a better way forward, you are doing the hard thing. I'm proud of you.

Drink your water, eat your protein, and be kind to yourself today.

See y'all,
Amy, Refinery Strength Collective

Research Behind This Post
Fairweather D, Frisancho-Kiss S, Rose NR. Sex differences in autoimmune disease from a pathological perspective. American Journal of Pathology. 2008;173(3):600-609. doi.org/10.2353/ajpath.2008.071008
Lemmey AB, Marcora SM, Chester K, et al. Effects of high-intensity resistance training in patients with rheumatoid arthritis: a randomized controlled trial. Arthritis & Rheumatism. 2009;61(12):1726-1734. doi.org/10.1002/art.24891
Santos EJF, Farisogullari B, Dures E, et al. Efficacy of non-pharmacological interventions: a systematic review informing the 2023 EULAR recommendations for the management of fatigue in people with inflammatory rheumatic and musculoskeletal diseases. RMD Open. 2023;9(3):e003350. doi.org/10.1136/rmdopen-2023-003350


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Meet Amy Karas

Hi, I’m Amy Karas—coach, mom, and believer in grit built over time. I help women cultivate durable strength through smart, compassionate training. After years coaching diverse women, I saw how many were under-served by one-size-fits-all fitness—especially those with autoimmune conditions or shifting seasons like postpartum or perimenopause. Refinery Strength Collective was born to change that.

Creds & Lived Insight:
  • NASM-CPT, Girls Gone Strong L1
  • Specialty: Autoimmune-aware, female physiology, power development
  • Philosophy: Faith-forward, science-driven, client-led
Values:
  • Dignity First – You are not your diagnosis or decade.
  • Evidence & Empathy – Data + lived experience guide us.
  • Progress Over Perfection – We refine; we don’t punish.
Photo of Amy Karas