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How to Use an Amazon Prime Membership to Save Money at Whole Foods

I know lots of folks who have an Amazon Prime membership, but only use it for the free shipping benefits and Amazon Prime Video. They’ve heard about the ability to get discounts at Whole Foods, but aren’t sure how it works or if it’s even worth it (especially those who do not already shop at Whole Foods). Maybe this is you too?

Whether you have an Amazon Prime membership or are thinking of getting one, this post gives you the lowdown on how you use Amazon Prime at Whole Foods and get the most savings possible on the best clean food items around!





When we think of Whole Foods today, what may immediately come to mind is a corporate behemoth that caters to the bourgeois. For the past 15 years or so, Whole Foods certainly has been synonymous with the idea that only “rich” people appreciate and can afford eating clean. But here at Clean Foodie, we know that EVERYONE, no matter their socioeconomic background, appreciates eating safe, clean food – especially after learning about the negative health effects of ingesting carcinogens and toxins on a daily basis.



Many of the restaurants and cafes profiled on Clean Foodie that exemplify the clean eating movement are as far from bourgeois as they can get! Indeed, these days there are exponentially more people who are making it a priority to eat clean, and finding creative, cost effective ways of doing so. Interestingly enough, it was a handful of people just like that who founded the original Whole Foods Market in Austin, Texas back in 1980.

I’m sure many of you are aware that Amazon bought Whole Foods in 2017. This was quite a coup in the grocery sector to say the least. Many people speculated what the delivery based behemoth would end up doing with the niche up-market health food store. Were they hoping to bolster their “Amazon Fresh” offerings? Was it simply a strategic move to secure distribution centers in densely populated areas?

Observing the transition seems to have revealed that it may be a combination of these things. But other long-term strategies will be revealed in time. Amazon has certainly made moves to increase Whole Foods’ reach beyond those little green dots on the map by carrying much of the Whole Foods 365 brand on Amazon and offering mind-bending next day delivery with a Prime Membership (which folks can Try Free for 30 days).

Convenience has overtaken the grocery sector as one of the top ways to draw new customers, with delivery becoming more prevalent in every aspect of the food service industry. And if there’s anything that Amazon knows and does well, its delivery.



Amazon Prime Whole Foods Membership Trial
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In order to take advantage of Amazon’s best delivery options for Whole Foods, becoming a Prime member makes all the difference. Prime members who live in the general area of a physical store can order groceries from Whole Foods on the Amazon website using a computer, the Amazon app or Amazon Prime NOW app, and get two-hour delivery, or 30 minute curbside pick-up. And if they spend $35 or more, the delivery fee is waived.

Just in terms of time and fuel alone, that’s great savings in itself. I’ll tell you how to get savings from exclusive deals in just a bit, but first let’s go over how to shop online at whole foods with your amazon prime account:


1) Sync your account with your local Whole Foods Store

This step is a piece of cake. Most times, your address will already be synced with the address on record with your Amazon Prime account. When you are at the Whole Foods page (either via the app or website), you will see a prominent “Deliver to….” box with your address. If not, or if you want it delivered to a different address (like when you are on vacation) there will be a link for “Find a Store” under the main menu. Put in the address, and you will be able to sync the nearest store.


2) Shop online and get your groceries delivered

Once your nearest store is synced, time to start adding groceries to your cart. As mentioned, you can use either a computer, the Amazon app or Prime NOW app to shop for delivery – all of which provide a highly user-friendly and intuitive experience. The Whole Foods app, on the other hand, cannot be used to shop online, but rather, is used to check current deals at your nearest Whole Foods, create lists, and for scanning your QR code at checkout in person.

When you are on the Amazon website, I advise to begin by searching through all the sale items first. Simply go to the Whole Foods link in the navigation menu and click the Prime Member Deals link. Once on the Deals page, scroll through the items and start adding to your cart. Outside of the deals section, be on the lookout for items on sale. As a Prime Member, you will get an additional 10% off the sales price:


Amazon Prime Whole Foods Deals
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As you add items, your shopping cart will begin to be populated, and calculate how much more you will need in order to qualify for free shipping:


Whole Foods Checkout
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When you are ready to check out, you will be prompted to include the best phone to use in case your shopper needs to substitute any items and clear them through you first (via text). Otherwise, you can opt to not allow any substitutions, and simply not receive an item if it is out of stock.

This is very important to keep in mind, as there are times in which the inventory online might not be 100% accurate at the time your shopper actually begins retrieving your items in the store. If this is the case, you will be pinged by text (or via a chat box if logged into your Amazon account on a computer), and given the option for a replacement item.

This has happened to me several times, and 90% of those times, I’ve gone with my shopper’s recommended substitution item. There may be a small price differential (the replacement item will cost more or less – but it’s usually negligible. This is actually why you will not be charged at checkout. Your card will not be charged until shopping is complete and potential substitutions are finalized.


Amazon Prime Whole Foods Schedule Delivery
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After picking your delivery window (they are released in two hour blocks throughout the day), I highly advise you keep your phone nearby and/or keep a tab open on your computer that’s logged into your Amazon account. If any substitutions are needed, you will need to respond in a timely fashion. If you do not reply in the time window, you will receive the recommended substitution.

Another great aspect of Whole Foods’ Amazon Prime delivery is the convenience factor when you’re in a bind. I have my own “Thank Goodness for Prime” story: When a family friend experienced a loss in their family, I wanted to offer some kind of comfort, but we don’t live nearby. It was after normal store hours, but I was still able to go onto Amazon and search within the Whole Foods nearest to my friend and put a selection of Whole Foods’ wholesome and comforting prepared foods into my cart and schedule it to arrive at my friend’s house after the memorial service the next day. I was so grateful that despite being last-minute, I was able to provide some healthy comfort to my friend when they really needed it.



Amazon Pantry 365 Whole Foods
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If you don’t want to bother with setting up a delivery time (which is obviously needed when ordering perishables), you can get just about every Whole Foods dry good under the sun by using Amazon Pantry (part of a Prime Membership). It’s just like ordering anything else at Amazon, except everything is organized in categories (breakfast, meals, snacks etc), and you will get the lowest prices available shopping for Whole Foods 365 signature organic brand.



Prime Whole Foods In Store Checkout Options
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I dare say that shopping at Whole Foods has become more attainable for me strictly due to my Prime membership. Most of you have probably heard the phrase “Whole Foods aka Whole Paycheck”. I witnessed the truth in that criticism first hand! I remember buying groceries at Whole Foods in the past and my jaw dropping at how two bags of groceries would eat up the majority of my grocery budget. It was years later, after catching wind of the new benefits Whole Foods was offering to Prime Members that I actually gave it a try again.

Here’s the deal – even with Prime discounts you are not going to save in comparison to somewhere like Walmart, Aldi, or some other discount grocery store. But you will have the opportunity to upgrade the quality of your groceries, have access to a wider array of specialty diet items, and choose more healthy, sustainable options while paying roughly what you would for a “normal” grocery shop at a “normal” grocery store. If you’re on this site and interested in the Clean Movement, it’s probably worth it to you.

One of the things I really appreciate about the experience of shopping at Whole Foods with a Prime membership is that it’s so freaking easy to find the Prime Deals! I don’t know about you, but I find it so annoying when I have to function like an investigative reporter just to find which items are on sale at the grocery store. Whole Foods doesn’t do that, they clearly label the Prime deals with a bright blue sign which makes them easy to spot.


Whole Foods Prime Deals in Store
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And we are talking some pretty dang good deals. Here are some examples from this past week:

  • Organic Strawberries, $2.99 (1-pound package)
  • Organic Fuji Apples, $1.49 per pound
  • Organic Asparagus $2.99 per pound
  • 20% off sustainable wild-caught Red Snapper Fillets

And these are just the examples of the Prime “exclusive” deals in the store, as each Whole Foods also has general sales on items they are looking to move more quickly, and Prime members get an additional 10% off those sale items as well. Click here to see what additional sales your nearest Whole Foods has right now.

The other way you can really get your grocery budget to stretch with a Prime membership is by getting the Amazon Rewards Visa Signature Card which gives you 5% cash back on all purchases including deal items you make at Whole Foods and Amazon. Now let me be real with you, I DO NOT recommend accumulating a balance on this, or any credit card.

This is what I’ve been doing to get the benefit of 5% cash back without paying interest: I set up the card as my payment method on my amazon account and set my autopay to pay off the entire balance every month. The next step requires being vigilant with keeping track of your purchases and making sure you stay within the monthly budget you’ve allowed yourself. It takes some discipline, but so does eating clean, so I know you can do it!



There are two ways in which you can be sure to get your Amazon Prime Whole Foods discount applied at checkout while in stores:


1) Give the cashier your phone number at checkout

But FIRST, you have to link your phone # to your Whole Foods Prime account. Doing so can get confusing, so pay close attention! It took me freakin’ 2 hours to figure it out. Updating your mobile phone # on your Prime Account will not do the trick. You have to add your phone via another area of the site (not available on the app). To date, I haven’t found a consistent way to navigate to this page, but HERE IS THE LINK. It looks like this:



At this page, click the “Update your mobile number settings” link. You will see the number that is assigned to your Prime account, but you still have to click the orange toggle next to “Use My Number at Checkout” to set it up:


Prime Whole Foods Update Phone Number
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2) Print the Deals QR code from your smartphone to your smart computer ahead of time.

Open either your Amazon or Whole Foods app, click the “In-store Code” link and take a screenshot with your phone of the QR Code. Print it off and wah-lah!

Now, if you’re wondering why you wouldn’t just bring your phone with you to the store and scan the QR code in person, so am I! I share the print option, just in case there are some die-harders who like to go off-the-grid at times, but who still need to eat clean (and save money!)

But if you never go anywhere without your phone, you might as well just use it at checkout (especially if you are using the Whole Foods app to find deals and check off a shopping list).


3) Scan the Whole Foods Deals QR code on your smartphone at checkout

Prime Whole Foods QR Code
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It’s that simple. Either open the Whole Foods app and touch the “Prime Code” link, or open the Amazon app and touch the Whole Foods link (a QR code pop-out should appear). Just hold your phone under the scanner and you’re off to the races!



Whole Foods Phone App
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You don’t have to use the Whole Foods app for getting deals with your Free Amazon Prime membership at Whole Foods, but if all you are looking to do is buy things on sale, this app could help you out.

Getting a five-star review in the app marketplace is like receiving a Michelin Star. Apps are not going to suit every single person’s needs.

Judging by app marketplace reviews, the Whole Foods app is probably not right for you if you’re looking for a comprehensive app that allows you to integrate a grocery list synced with 100% of inventory. But that’s not what the app is designed to do, and imo, it’s not entirely fair to give it a one star rating simply because it’s not a shopping app with all the bells and whistles.

The gist of the 5-star reviews, on the other hand, is that the app does what it’s supposed to do. It’s minimalist by design – solely used for checking deals at specific Whole Foods stores.

Simply scan the Whole Foods code at checkout instead of handing a bunch of cutout coupons to the cashier. It also offers the ability to create a shopping list (much like the app Wunderlist), the only caveat being that it is not integrated with a particular store inventory.

My advice is to think of the Whole Foods app as a digital sales flyer that you can check before shopping. This is especially of value for Amazon Prime members. There’s no need to wander around the store, looking for the iconic “Prime Members Save” signs.



Okay, now that we’ve figured out how to make the high quality offerings at Whole Foods more affordable by using a Prime membership in conjunction with an Amazon Rewards card, let’s discuss how shopping at Whole Foods may help you on your clean journey.

It all starts with those hippies in Austin back in the 80’s. They started out with a mission to sell the highest quality natural and organic foods and today they state on the Whole Foods website, “Our product quality standards lead the marketplace. We focus on growing methods, safety, ingredients, taste, freshness, nutrition and appearance.”

But what really helps me relax when I shop at Whole Foods is their list of unacceptable ingredients. They have made a commitment to not allow these things in the items they stock in the store. This list covers a ton of items known to be dangerous and/or inhumane, things like hydrogenated oils, high fructose corn syrup, foie gras and over 100 other coloring agents, preservatives, and additives. Still, you’ll always need to read labels to ensure you’re sticking to the specific diet that you are maintaining, but knowing that Whole Foods has done a lot of the screening work for you, makes the shopping process so much easier.

When we take that kind of attention to detail and quality into account, it starts to make sense why Whole Foods is not, nor will it ever be, the cheapest grocery store in the world. With every passing year I come to appreciate the truth in the phrase, “You get what you pay for”.

But it can be a real challenge when consumers are bombarded by designer brand items that are cheaply made but still sport high price tags simply in the name of “prestige”. Knowing when it’s worth paying a little more takes serious due diligence. And something that helped me determine if it was worth paying more at Whole Foods is their commitment to valuing their suppliers in a way that supports the sustainable and organic practices they’re trying to uphold.

Whole Foods has a Local Producer Loan Program that has forwarded $25 million of regional market capital in the form of over 350 loans to small independent local producers. When I think of that, it makes so much sense to me why the prices at Whole Foods aren’t dirt cheap. Because maintaining safe, nutrient rich dirt isn’t cheap. It takes a lot of effort, and manpower to sustain organic and biodynamic farms.

There is a reason factory farming became the norm; because it’s easier. The fact that Whole Foods is willing to invest in helping more farmers and producers to go organic and become committed to being animal compassionate helps me make the choice to invest in them by buying some groceries when I can afford it.

Clean Foodie has a mission to make it easier for everyone to find food that is truly safe and healthy. Hippocrates wrote, “Let food be thy medicine” and we agree with that 100%. Whole Foods has set standards for all the products it carries, which makes it so much easier to make smart healthy choices. They take these standards so seriously that Whole Foods is actually the first, and currently only, Certified Organic national grocery store. They were able to achieve this by not just taking a food brands word when they say they’re organic.

Instead, they make sure if something is labeled organic that it was grown with those standards, picked, processed and shipped with those standards as well. They even make sure that the individual ingredients in products used in their kitchen for organic prepared foods meet those standards. Basically, Whole Foods has taken it upon themselves to be the “investigative reporter” so I don’t have to be.

Beyond ensuring that their customers have access to high-quality healthy food, Whole Foods is acting on a vision to make these things available to people beyond the walls of its stores with the Whole Cities Foundation, Whole Kids Foundation, and the Whole Planet Foundation.

The Whole Cities Foundation is dedicated to working with community non-profit organizations in order to build thriving and healthy local food-systems and increase the health of the community as a whole.

The future of our communities is dependent on the health of our children, which is why the Whole Kids Foundation really stands out as a tangible positive investment. This foundation provides grants to schools in order to help them provide healthy food to their students, plus build educational vegetable gardens, set up lunch salad bars, offer nutrition classes for teachers, and even cultivate honey bees!

Something our children will come to know well is how interdependent we all are on this planet, which is why the Whole Planet foundation serves to strengthen the prospects of communities worldwide by providing micro-loans to individuals who live in the poorest areas. The average size of the micro-loans it provides is $178 USD, but with these small amounts, individual families are able to create a business for themselves and slowly work their way out of a cycle of poverty and instead provide a future for their children that lifts their community as a whole.

Whole Foods Foundation Haiti
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Benita in Haiti was able to buy ingredients to make pastries with her loan. She continued to work hard and was able to pay off that first loan in order to get another until she had saved enough to build a roadside store in front of her home. With the profits from her store, she has been able to invest in livestock which will help ensure the financial security for her children in years to come.

Learning about these foundations and the amount of effort Whole Foods puts into ensuring the quality of their products helped me see the value in being a Whole Foods shopper.The fact that I can take advantage of Prime deals and the 5% cash back from my Amazon Rewards Visa Signature Card is just the cherry on top at this point.



Four young “hippies”, John Mackey and Renee Lawson Hardy (co-owners of Safer Way Natural Foods), Craig Weller and Mark Skiles (co-owners of Clarksville Natural Grocery) joined forces to open the very first Whole Foods Market with 19 staff members in a 10,500 square foot space.

Whole Foods Original Store
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It was important to this young and energized group to create a “real” grocery store focused on safe, healthy and wholesome products, and not just a shop selling vitamins, powders, and potions.

But no good deed goes unpunished as they say, and a year after the store opened, it was devastated by a flood. Despite not having flood insurance, they were able to pull together donations from the community and convince lenders to give them a second chance. The first Whole Foods was able to open its doors again only a month after losing everything. This makes it pretty miraculous that in four short years they would start expanding and opening Whole Foods Markets outside of their hometown of Austin.

A big part of Whole Foods’ growth was due to merging with locally owned organic health food stores in other regions. They built a solid foundation with stores that already had a dedicated clientele, and were thus able to reduce their risk as they expanded into new markets. Today, Whole Foods has over 500 stores in the United States, Canada and the United Kingdom.

And with a much heightened online presence thanks to Amazon, Whole Foods is becoming increasingly competitive in terms of cost, and fast becoming the go-to grocery destination for the best in clean and organic food.

Whole Foods Prime Membership Review
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