Why Can’t Subway Be Like Chipotle With Food Allergies?

This question has vexed me for years. Despite being two different types of restaurants – Chipotle, a fast-casual Mexican restaurant, and Subway, a quick-service sub shop – the setup of each is similar with what I refer to as an assembly line process of creating a guest’s meal. In just looking at their food preparation line and frequenting each restaurant often, one would think that they’d have similar abilities to accommodate food-allergic guests. However, they don’t. Chipotle is a perennial inhabitant of a spot on AllergyEats’ Top 10 Most Allergy-Friendly Restaurant Chains in America list with an overall AllergyEats allergy-friendliness rating of 4.28. On the other hand, Subway has a dismal AllergyEats rating of 3.08 of 5 (US only). So, I decided to call a handful of Subway AND Chipotle restaurants in markets across the US and ask the simplest of questions for comparison.

Both Use An Assembly Line

Both Chipotle and Subway start building a guest’s meal on one end of their food prep line with the “container,” as I’ll call it (sandwich bread, tortilla, bowl, etc.). They each place it on foil (Chipotle) or paper (Subway). They each then slide this “container” down a counter of food, adding products the guest wants as they go. The main proteins and other key ingredients are assembled in the first half, with “toppings” added in the second. (e.g. For a burrito, I might put chicken, black beans, and brown rice on in the first half, with salsa, cheese, and sour cream added in the second. Or for a sub, ham and cheese at the beginning, with lettuce, onions, and pickles at the end.) The final product is then wrapped and ready to go.

Subway vs. Chipotle with Food Allergies

A burrito being made on the Chipotle assembly line.

So you see, the restaurants are seemingly very much alike. Now, let me point out a few differences. Subway has a toaster that they use in the middle of the prep for some subs. Chipotle’s food is generally “scooped” from containers, whereas Subway’s sandwiches are assembled by hand (the meats separated by paper for proper proportions). For liquid or semi-liquid toppings, like vinegar or mayo, Subway has squirt bottles, where Chipotle uses a ladle to again scoop queso sauce, hot salsa, and other liquids.

Subway vs Chipotle with Food Allergies

A Subway sandwich being made on the assembly line.

Of the major allergens, Chipotle is probably most challenged by dairy and wheat. Subway is also challenged by these, though they also have to consider soy (in several items), and occasional egg, fish, shellfish, and even tree nuts & peanuts (in cookies). That said, given the assembly line style of preparation and the standardized food products delivered to their store (such that they have an allergen chart applicable to the whole country), I still believe that Subway should be able to accommodate the food allergy community as well, or close to as well, as Chipotle.

Cross-Contact Comparisons

In my opinion, Subway should also have a lesser chance of cross-contact by far. Their food is much less likely to spill and they don’t ladle liquids, choosing instead for a controlled squeeze bottle. The toaster is a risk, but even that can be easily accommodated. The biggest risk should be the potential for cross-contact in the “toppings” area given the use of hands to pick up the food, though even that should have an easy work-around. On the flip side, Chipotle has food that can fall all over the place and liquids that can easily be spilled as they’re ladled across the counter to your food.

So, in the final comparison, I would say Subway and Chipotle each have an easy-to-manage assembly line food preparation area, Subway has a slightly greater challenge of managing more allergens, and Chipotle has a greater cross-contact risk. Advantage? I’d say Subway.

So why does Subway only have a dreadful 3.08 AllergyEats allergy-friendliness rating versus Chipotle’s amazing 4.28? Even other fast food chains are a half point higher than Subway!

As always, it comes down to commitment from management. In this case, I would also add the issue of Subway being a franchised chain as opposed to Chipotle, where the company owns all its restaurants.

Consistency is Key When It Comes to Food Allergy Dining

I am a regular at Subway because my son, despite having tree nut, dairy, and sesame allergies, loves eating there (and we’ve learned how to navigate them). He actually feels safe at Subway because he can see them prepping his food and he can tell them what to do if they’re about to inadvertently make a mistake (which happens way too often). Due to my experiences there, I can tell you that the employees are simply not trained in any responsible way by management, if at all.

I am also a regular at Chipotle and, as most of you have experienced, they clearly have set procedures and protocols in place that are followed to a T most of the time.

Beginning with Subway, every experience I have there is a new adventure. Most of their restaurants don’t have a copy of the ingredient list on the premises, and most don’t even know there’s one online. (That list is important and extremely helpful. Pull it up on your phone if you visit Subway.) Employee reactions when I tell them we have a food allergy? Most often I get a look of “uh, so, why are you telling me that?,” but in fairness there are some who know the next step if nothing else – changing gloves. For those employees who don’t, I ask and they usually do so without questioning – though I have had some who balked at first. And so on down the line. Unfortunately, I don’t think they have a procedure in place to get fresh “toppings” (lettuce, onion, pickles, tomato, etc.) from the back to eliminate cross-contact risk. Why? That should be easy!

At Chipotle, I disclose an allergy and the machine is in motion. Gloves are changed (hands sometimes washed in the middle), allergy is announced, request is made if the customer wants food taken from the back (to prevent their biggest risk – cross-contact – mentioned earlier), and often the same person handles the meal down the whole food prep line to prevent any other cross-contact risk.

I emailed Subway and asked if I could speak to someone about food allergy procedures and for information beyond the allergen chart they have online. They forwarded me the link to the Nutrition & Allergy info on their website. Very nice. I emailed again with more detail and got a call back. The representative told me she wasn’t sure what each individual franchise owner requires or does in their store with respect to food allergies and that I’d get a call back from the regional office with 2 days to speak with someone more knowledgeable. That call never came, but it was clear that there is NO corporate policy.

So, to see if my experiences were a fair representation, a colleague and I called Subway AND Chipotle restaurants across the US (in many different markets and at different times). Basically, we asked if they have food allergy procedures, if they have a food allergy chart (which I knew Subway did), and what they will do if I came in later with my dairy-allergic son.

Over 80% of those answering the phone at Chipotle (most not needing to get a manager) not only knew they had food allergy procedures, but could rattle them off easily: wash hands, change gloves, clean surface, get clean utensils, get protein from the grill (where no dairy is ever present).

Subway’s answers were, like my experiences, all over the map. Knowledge levels varied dramatically employee to employee.

Many admitted (thankfully) that they didn’t know what to do. Regarding food allergy protocols, too many said they had no idea about any, though some were able to redeem themselves with a manager’s help. When prompted, a decent number knew that they should change gloves, use new knives, and wipe down the prep area with a rag and “sanitizing solution.” That was positive. Unfortunately, almost none knew they had a food allergy chart and, to make it worse, MOST thought there was no dairy in any of the breads. In fact, about 1/2 of their breads contain dairy! Regarding the toaster, answers about preventing cross-contact using the toaster (which they can) were completely inconsistent. But the best answer in the bunch was the employee from Utah who said they’ve never had a food-allergic customer… ever. There are 32 million of us – someone must live in Utah!

In the end, it seems as though the way to navigate Subway safely, as my son has for years, is to take control yourself. Check their allergen chart on your phone, tell them exactly what you need them to do with respect to gloves, utensils, etc., and watch them like a hawk for mistakes. (Of course, you should watch all restaurants prepare your food when possible, not just Subway.) Depending on your level of comfort, you may want to avoid “toppings” altogether.

The other catch is that they’re a franchised organization – and a HUGE one at that (the largest in the world!). This is not to say that all franchised restaurant chains are bad with food allergies (an analysis we’ll be sharing with you soon). It is to say, however, that weak requirements by central management lead to even weaker actions by the individual owners of a franchised organization. In other words, if Subway’s corporate office doesn’t dictate strict policies on food allergies (like they do with the setup of the store, the meal prep line, the way the food is prepared in general, etc.), then each restaurant is on its own. Again, some franchise chains do a great job, but the potential for failure without corporate-level protocols is much greater – and Subway is exhibit A.

Being Food Allergy-Friendly is Smart Business

Every restaurant or chain owner has the right to operate their business as they see fit. I’ve always been a believer in that. I don’t believe restaurants have to be allergy-accommodative in any way if they so choose and I respect the rights of those restaurants who rely on a certain allergen or type of cuisine as part of their concept (e.g. Five Guys with peanuts). That said, it doesn’t take someone with my financial background to recognize the foolishness of not catering to our food allergy community – a very vocal, very loyal community of diners who stick to those restaurants and chains we feel most comfortable with. I’ve done the math many times and can say with a high level of confidence that being allergy-friendly can boost a restaurant’s profits by up to 25% or more! That’s a ridiculously high number given the nature of the restaurant business.

Given the ubiquity of the Subway brand around the US – and the world – it’s disappointing that they don’t recognize the value of our community. Clearly, as Chipotle shows, Subway can be allergy-friendly. How great would it be if all 27,000+ Subway restaurants in America were a place where the food allergy community could feel comfortable? With roughly 8x as many US restaurants as Chipotle, and one seemingly every few exits on the interstates, navigating our allergies would be that much easier.

For now, however, proceed with caution at Subway. They are no Chipotle.


What do you think? How is your local Subway? Are they one of the good or one of the not-so-good? Share your story here.

And don’t forget to rate all your restaurant experiences on the AllergyEats app or website – whether Subway, Chipotle, or any other restaurant in the U.S. Each new rating makes AllergyEats more valuable for our entire community.

We’re all in this together!


    Kristy-lynn Bakke

    Subway has never seemed to care to try and incorporate safe food allergy policies. It’s fine, I know that not every place is going to accommodate. There’s lots of other places, sandwich places that do.
    But we love tex mex, so if we’re going out to grab something, it’ll be Chipotles.


    I had a *horrible* experience with Chipotle and will never eat there again because of potential gluten cross contamination — and because of the lack of concern in response to my complaint to their home office. After seeing a gloved employee resting her hands on the tortillas, I suggested to the home office contact that they try to move the tortillas to another location (currently located next to the salad greens) where the chance of cross contamination with the salad and everything else could be avoided. The contact told me, pretty much her words — that’s the way it has always been and we aren’t going to change it. They just don’t get my business anymore.


    I appreciate this story, but it would be helpful if you could have also addressed the cookies at Subway. It is my understanding that they bake the cookies and the bread on the same cookie sheets, so I have never been comfortable with my nut allergic daughters eating at Subway. And as you say, the Subway employees seem to have no knowledge of food allergies, and the ones in my community do not speak English either, so we don’t eat there.


    Did you find out if subway has a procedure for baking the cookies with peanuts and tree nuts? I know everyone has different allergies, but why in the world do they have to keep the dumb peanut butter cookie??


    EVERY food establishment should have employees that Serve Safe certified. This class teaches them how to avoid cross contamination and take allergies and autoimmune issues seriously.
    My daughter runs a Baskin Robbins and she is Serve Safe certified and has trained her staff. She was a safety freak even before her Mom got diagnosed with Celiac. Her customers thank her all the time for taking care of them and their loved ones.
    Baskin Robbins has easy to access information on their products. I don’t understand why it’s so difficult with other restaurants. Frankly, I would be terrified to eat at Subway. Trust is huge when your food can actually hurt you. I have a handful of managers I trust with my health. If you’re ever in Mountain Home, AR stop by El Chico Cafe – Sandy Luna, the Manager, is a rock star of food safety!! Or Baskin Robbins…and ask for Cait!

    Laira Biestaad

    Thank you for your article! Have you noticed that some of the unknowing employees do sometimes take offense to your allergy requests and treat you like you have offended them???
    I have had it with restaurants, period because I don’t feel safe, and who knows what is happening to my meal. Unfortunately, or fortunately; I always bring my own food EVERYWHERE I go, and just get ridiculed. It’s disparaging.

    Laurie Pipitone

    Thank you for this article. I found it very interesting. I have never eaten at Chipotle, but will have to check it out. My daughter has celiac disease and it is very hard to trust most restaurants. We have a local subway shop that actually carries gluten free buns for $1 extra. We frequent that location, but it’s the only location we know of that has them and it’s because they have gluten allergies in their family/friend circle. However, their employees are not trained for the allergy and have no clue what to do except for changing the gloves. Many times we have gone in there and they are out of the gluten free buns, or they don’t have any thawed and I have to tell them how to thaw them. It’s extremely frustrating. I wish more restaurants would consider those with allergies, especially with how common it is now days. These people just want to be able to go out and have a nice safe meal just like anyone else.

    Joan Richard

    Why can’t Mod Pizza be like Blaze Pizza? If you didn’t see their name on the door, you’d swear it was the same place. Although Mod claims to be “gluten friendly”, I was told that it was only for “life style” choices. They changed their gloves and then proceeded to use all the same utensils as they normally would. Blaze, on the other hand, is fantastic, and go the extra mile to ensure food safety. Exact concept, but the difference is in the management and caring staff.


    Subway is beyond horrible with cross-contaiminarion with their seafood concoction that flings little bits of potential death about every time they use that ice cream scoop of doom.

    They also have that dirty knife that they use to cut every sandwich, which is cleaned with an even dirtier rag.


    My son is 12 and allergic to milk, eggs, peanuts, and tree nuts. Our local Subway often will host “school nights,” where a portion of the proceeds go to the local schools, and he always wants us to go to the shop on those days, but he will only get a bottled drink and packaged chips. He will not get a sandwich or wrap because he does not have any confidence that they will be able to accommodate him based on watching them prepare food for me and his dad.

    Unfortunately, even if the corporate level has a commitment to food allergy safety, if the franchise owners are not committed as well, cross-contamination risks will abound. Conversely, one of my son’s favorite places to go is Taco Bell. One would think that, with the ubiquity of cheese in Taco Bell’s menu, that the restaurant would be a death-trap for my child, but the local owners of Taco Bell have committed to being allergy friendly, and the employees at our local store will go into “allergy protocol mode” as soon as they see us walk in the door!

    For assembly-line style restaurants, it is easy for them to do what is necessary to make accommodations, but without proper instruction down from the top, it just will not happen. Thanks for the deeper dive investigation into Subway!

    Frank Coluccio

    In NJ we have Jersey Mike’s subs that handle food allergies well with dairy, soy and egg free ingredients like gluten free bread and cold cuts. That beats Subway by a mile.


    Our local Subways have told me they use the same baking trays for (peanut and tree nut containing) cookies as for bread, and just wipe them with a dry cloth between uses. Why?! It would be so easy to have dedicated trays.

    And while I love Chipotle and we’ve had good luck there overall, we’ve had what someone above mentions happen to us several times: immediately after washing their hands and changing gloves for gluten precautions, the employee will rest both hands ON the stack of giant WHEAT tortillas! It’s happened multiple times in different locations/states so I watch for it now.

    Gail McNiece

    I spoke with a Subway in MA. They bake the peanut butter cookies on the same sheet pans they use for the bread. I was told that the pans are “supposed to be washed” between foods. Only one person working at the time seemed to be aware of this, so we don’t ever go to subway.


    As another option to Subway, I’ve had very good experiences are Jimmy John’s for my top 8 allergic kids (one is mildly allergic to wheat so it’s less of a concern for us and soy isn’t an issue). They have always been willing to change gloves, wipe down the working space, and lay extra paper down before getting our sandwiches together.

    Jersey Mike’s doesn’t have a dedicated slicer for dairy so it’s not an option for our family.

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