HomeHealth TopicAutoimmune Disorder

What to Do When Your Treatment for an Autoimmune Disorder Isn’t Working

Christina Palmer, MD
Published on March 10, 2021

Key takeaways:

  • Treatments for autoimmune diseases can be complex and often need to change.

  • These treatments can have side effects and risks, and you should know what to look out for. 

  • Your diet and lifestyle could play a role in the success of your autoimmune treatment.

  • If your current treatment is not working for you, it’s important to have a discussion about treatment alternatives with your provider.


Autoimmune conditions such as rheumatoid arthritis, lupus, multiple sclerosis, and psoriasis can be hard to diagnose and even harder to treat. While they all share the common underlying issue of your body attacking its own cells, there are over 100 autoimmune conditions and they can vary greatly in their symptoms and severity.

Likewise, there are many treatment options for autoimmune diseases, and it’s important to understand what they are, what to expect from them, what lifestyle factors may play a role, and what to do if treatments aren’t working. 

What medications are used to treat autoimmune diseases?

When you have an autoimmune disease, it’s important to understand why you are taking certain medications, and what their role is in your treatment. This will help you set expectations for therapy and understand when you may need to make a change.

Symptom management

Some medications are used to help with symptom management only, and they won’t affect the underlying disease process in your body. They can help with things like stiffness, pain, and swelling in your joints. Here are some examples of these medications.

Oral medications

Pain relievers such as acetaminophen (Tylenol) can help with pain, whereas nonsteroidal anti-inflammatory drugs (NSAIDs) like ibuprofen (Advil), naproxen (Aleve), and celecoxib (Celebrex) can help with pain and also help lower inflammation. 

Celecoxib is only available by prescription. Ibuprofen and naproxen are both available over-the-counter (OTC), but you can get higher strengths with a prescription as well.

Topical medications

Some medications can be applied directly to areas of pain to provide relief. These include topical capsaicin or topical NSAIDs like diclofenac gel(Voltaren).

Steroid medications

Steroids can help lower inflammation and pain in the short term, but they are generally not recommended long term due to side effects. They are available in oral, topical, and injectable forms. Examples include prednisone, dexamethasone, and methylprednisolone.

Disease-modifying treatments

Some medications treat the disease itself. These are called disease-modifying treatments, and they work by suppressing your immune system. This targets the underlying disease process and can help slow the progression of an autoimmune disease. You may be on these medications for months to years, and they can take time to start working.

These medications can include, but are not limited to the following.

Disease-modifying antirheumatic drugs (DMARDs)

DMARDs used to treat autoimmune diseases like rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) can be broken down into two groups: conventional DMARDs and biologic DMARDs.

Conventional DMARDs are typically the first choice for treatment, and they include medications like methotrexate, hydroxychloroquine, and sulfasalazine.

Biologic DMARDs may be used when conventional DMARDs alone aren’t working as well. They are a different type of DMARD that blocks a specific part of the immune system. 

Biologics are typically injectable, and they include medications like Enbrel, Orencia, and Humira. Xeljanz is a newer biologic medication that is available as an oral tablet.

Other disease-modifying drugs (DMDs)

There are additional disease-modifying drugs (DMDs) for multiple sclerosis (MS), and they include oral, injectable, and infused medications such as Avonex, Copaxone, Tecfidera, Aubagio, and Ocrevus.

Which treatment options will work the best for me?

Your treatment options will depend on which autoimmune disease you have or your specific symptoms. Some autoimmune diseases such as type 1 diabetes or Hashimoto’s disease attack a specific organ system (like your pancreas or thyroid), so you may need to take a replacement such as insulin or thyroid hormone. Cost and insurance coverage can also affect your options. 

Keep in mind that treatments often need to change over time — your disease may require new therapies or you may not tolerate the side effects. 

How can you tell if your treatment isn’t working?

You may be able to tell if your treatment is no longer working if you notice more symptoms or flares of your condition. Each autoimmune disease is unique, but you may have more joint pain in rheumatoid arthritis, fevers or fatigue with lupus, numbness or blurred vision in MS, or stomach pain and diarrhea in IBD. 

Is it a side effect, or is my treatment not working?

Sometimes it’s hard to know if the symptoms you are experiencing are related to your autoimmune disease flaring or to side effects of your medication. Either way, it’s important to describe what you are experiencing to your provider.

The disease-modifying treatments for autoimmune diseases can have many side effects, such as nausea, diarrhea, liver problems, or rash. Each of these medications has its own possible side effects so it’s important to know what to look out for. 

Since disease-modifying treatments work by suppressing your immune system, you’ll also have an increased risk of infection. This includes viral or bacterial infections, or even reactivating a prior infection like tuberculosis or hepatitis. Symptoms like body aches, swelling, and stiffness from an infection may seem like a symptom flare, so you’ll want to make sure that your provider knows what’s going on in case you are sick. 

If you have flares or progression of your autoimmune disease, then your treatment may not be working as well. For example, you may have uncontrolled pain, fatigue, or limited mobility. If this happens, it’s time to take the next step in your treatment plan.

What can cause a treatment to fail or be less effective?

It’s often unknown why a certain treatment for an autoimmune disease may not be effective, but it’s not uncommon. About 30% to 40% of people taking biologic medications end up stopping them because they aren’t working as well or due to side effects.

In some cases, your body may have developed antibodies against the medication This means that your body sees the medication as an invader, which can cause it to not work as well for you. And there may be other genetic or immune system factors that we can’t yet identify, too. 

Taking your medications consistently is also important so that you get the most benefit, but sometimes there are barriers, such as high medication cost or limited insurance coverage, that make it difficult. There could also be behavioral factors that impact treatment such as a poor diet, high stress levels, or not getting enough sleep.

Is there anything I can do to make my treatment more effective?

Being diagnosed and treated for an autoimmune disease can make you feel like your health is out of your control. But it can be empowering to realize that there are steps you can take in your lifestyle or diet to take control of your disease. It may be helpful to work on these at the same time as you explore additional treatment options with your provider.

Dietary factors and vitamin levels

Dietary factors likely play some role in autoimmune diseases. And there is some evidence that dietary changes, such as an elimination diet called the Autoimmune Protocol (AIP), could help symptoms and inflammation levels in IBD and Hashimoto’s disease

Scientists are still studying this, but it may have to do with improving the health of the gut microbiome and strengthening the intestinal lining. This helps to provide a more effective barrier against toxins and microbes entering the bloodstream, thus helping to prevent what is sometimes called “leaky gut.” 

You also might want to consider your levels of Vitamin D, which plays an important role in the healthy functioning of your immune system. Low levels are associated with both cancer and autoimmune diseases. It’s worth discussing your level with your provider and how best to supplement if it is too low.

Staying active

Exercise is generally safe in most autoimmune diseases, and it can help improve fatigue, mood, mobility, and quality of life. The amount and intensity of your exercise regimen will depend on your condition, but moving your body and getting your heart rate up every day is helpful. Try to listen to your body and do what feels right. If you need help finding a place to start, look into exercise classes (in-person or online) that are geared towards people with your condition.

Getting enough sleep

Fatigue is a big issue for many people with an autoimmune disease, and sleep is an essential part of keeping our immune system healthy. Make sure to practice good sleep hygiene and try to get at least 7 hours of quality sleep every night.

Stress management

High stress can impair immune function and may lead to the development of autoimmune diseases, as well as play a role in effectiveness of treatment. Working on stress reduction is important, and it can have a positive effect on your condition.

There may be other factors in your life besides the ones listed above that are impacting the control of your autoimmune disease. For example, you may have other active health conditions or mental health challenges, social or financial stressors, or barriers to accessing the providers and medication that you need. Try to identify what those barriers are for you, and consider discussing them with your support network and healthcare team in order to get the help you need.

What is the best way to approach your provider about alternatives?

If you experience more pain or flares of your condition or intolerable side effects from your medication, or if you face other challenges or concerns preventing treatment from being effective, it’s time to have a discussion with your provider about next steps.

Having this conversation with your provider is not always easy. And it is completely normal to have concerns like:

  • You’re not being listened to. 

  • You don’t understand what your provider is saying. 

  • You’re not comfortable in the medical office. 

  • You don’t have enough time with your healthcare provider during visits. 

  • You feel judgement or stigma. 

And if you’re part of a community of color or other underrepresented group, not only may you be at increased risk for certain autoimmune diseases, but you may also face additional challenges in getting the care you need.

When you live with an autoimmune disease, it’s important to learn how to be your own medical advocate. This means you understand your healthcare needs, and you are willing to speak up on your own behalf. 

Tips to help you prepare for your appointment

Here are some ideas to help make your appointment successful.

1)Prepare for your appointment with an agenda and your questions written out. This can help guide the discussion and make sure that all of your questions are addressed.

  1. Practice asking some of the hard questions, such as:

“I have concerns about my current medication. Can we discuss other treatment options?”

“Can you help me understand how my treatment is preventing progression of my disease?”

“What are some actions I can take in my diet or lifestyle that might help my disease?”

“I think my depression and anxiety are impacting my autoimmune symptoms. Can you help me find treatment for that so I can improve my overall health?”

  1. Consider bringing a support person to your visit.

  2. Plan to ask a lot of questions during your visit. Remember that any question is a good question.

  3. Consider requesting telemedicine visits for close follow up with your provider. Telemedicine may enable you to see your provider more frequently, and it may be a more comfortable way for you to voice your questions and concerns.

  4. Make sure you feel like you are a part of “shared decision making” with your provider and that you feel good about the plan made. If you have concerns, speak up. It’s OK to disagree.

  5. Be prepared to take notes during your appointment. 

  6. Don’t end the appointment until you are sure you understand your provider fully.

  7. If you’re not satisfied with your visit, don’t be afraid to find a new provider, ask for a second opinion, or request referral to a specialist. 

The bottom line 

Autoimmune diseases can be challenging to diagnose and treat. There are many treatment options, and they often need to change. Treatments can have many side effects and risks, too, so make sure you know what to look out for. 

Think about what actions you can take in your diet or lifestyle to improve your treatment success. If you find you’re not getting the results you need, it’s time to have an honest conversation with your provider about next steps.

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