Whole Foods stores are facing widespread food shortages, leaving shelves bare and customers angry. While many are blaming Amazon, which bought the grocery chain in August for $13.7 billion, employees say the problem predates the acquisition and is actually caused by the company’s “militaristic” new inventory management system.

Barclays analysts, who completed Whole Foods store checks across the Midwest earlier this month, reported “high” out-of-stock issues on both branded and private-label items, Business Insider reports.

While they note the lack of stock could be a result of increased sales since the Amazon acquisition, they suggest it’s being handled poorly.

REDDIT THREAD SLAMS APPLEBEE'S WITH SCATHING REVIEWS

"This is a high class problem if in fact sales have really accelerated — but is also an execution issue resulting in lost sales," analysts said.

Analysts also commented on the size and quality of produce, reporting that it “appears to have deteriorated.” They did however acknowledge this could’ve been related to the winter storm at the time, but customers and employees seem to agree.

"At my store, we are constantly running out of products in every department," an assistant department manager of an Illinois Whole Foods told Business Insider. "Regional and upper store management know about this. We all know we are losing sales and pissing off customers. It's not that we don't care — we do. But our hands are tied."

Other employees agree, attributing the lack of stock to the store’s order-to-shelf (OTS) buying system that was implemented last year. With the new OTS, less food is stored in stock rooms and instead it largely goes from delivery trucks straight to the shelves.

"The system is now set up to pretty much only have enough product to keep the shelf full and no extra," an employee of a store in Sacramento, Calif., told Business Insider. She also said her back-stock area had reduced in size by about 25 percent.

Employees also say the strict rules they must abide by with today's OTS are crushing morale and one person even went so far as to call the system “militaristic,” according to Business Insider.

The streamlined system has reportedly helped reduce food waste and saved the company money, but it’s also leaving customers frustrated with the lack of inventory.

"I get constant and consistent complaints from customers for continuously being out of staple [products]," the Sacramento employee told Business Insider. "It's frustrating as an employee and also as a shopper."

Social media is flooded with pictures of empty produce bins, bare meat counters and sparse shelves at Whole Foods stores across the country.

FOLLOW US ON FACEBOOK FOR MORE FOX LIFESTYLE NEWS

Whole Foods did not immediately respond to Fox News’ request for comment, but the company's vice president of operations, Ken Meyer, said in February that the new OTS has transformed the inventory levels in the back room, "essentially clearing them out so that we're mainly focusing on what we call our never-outs, the key items that we need to have in stock all the time in our stores."

"It's creating a really strong, efficient process from the way the goods are received in the back door to bring them right out to the shelf. And it's really improving and helping our out-of-stocks as well — dramatically," he said, as quoted by Business Insider.