FBA Fees Are Rising. What Can B2B Manufacturers Do About It?

Here’s an interesting and noteworthy fact about Amazon: It seems to continue to grow relentlessly, no matter what is happening in the world. The company’s 2025 net income hit $77.7 billion, up 31 percent from $59.2 billion in 2024, which itself was up 94.73% from 2023.

Some of that income has come from simply winning more sales. After all, Amazon is now the go-to search engine for both B2C and B2B products, and it’s been years since it grabbed that title from Google.

But increased sales isn’t the only reason why Amazon continues to report record profits. Two years of steep growth, and sellers are footing part of the bill, especially if they’re using Fulfillment by Amazon (FBA).About two years ago, Amazon set its sights on improving its own profitability, and that has largely come at the expense of sellers. For example, in 2024 Amazon introduced a new low-inventory fee, an inbound placement fee, and a returns processing fee. Reimbursements got cut 75 percent heading into 2025. A 3.5 percent fuel surcharge landed on top of fulfillment fees in April 2026. One industry tracker puts total fulfillment fee growth at over 30 percent since 2020.

Clearly, there’s a trend here, and we believe Amazon will continue to raise prices on sellers. And that means, if you’re going to sell on Amazon, you will need to know how to cut expenses to protect your own profitability. Here’s how.

How to Lower Your FBA Fees

1: Track Your Fees

Being profitable on Amazon reflects all your fees, including fulfillment fees, storage fees, referral fees, and other charges. Which is why you should create a P&L specific for your Amazon program that breaks down all your expenses line by line. 

Manufacturers who get blindsided by a fee change are usually the ones who were only checking overall profitability, not watching individual line items.

It’s important to note that Enceiba tracks and benchmarks these fees for clients. We know what you should be paying. We will alert clients when a fee structure changes, so they’re not finding out three months later that their margins slipped.

2: Stay on top of Compliance with Amazon

Fee increases are annoying, but compliance violations can be even more expensive. Amazon charges sellers for mislabeled products, incorrect packaging, and shipping errors. Making these mistakes often will stack up charges quickly on top of everything else already eating your margin.

We've taken over accounts buried in exactly this kind of mess. Cleaning it up costs money. Worse, it costs time; i.e. time your product sits unsellable while you sort it out. That's lost revenue on top of the fees.

It’s essential to get the basics like labeling, packaging, shipping requirements right. It's cheaper to follow the guidelines than to fix what happens when you don't.

3. Control What You Can Control

You can't stop Amazon from raising fees, but you can control your pricing, your fulfillment method, and your product-level economics.

Start with pricing, including B2B pricing. Set prices too low and every fee increase cuts deeper. Set them too high and you lose the sale. Take the time to figure out the sweet spot that takes into account your true FBA costs. And do this for every single product in your Amazon Assortment. Determine which products are actually profitable and which aren’t and monitor on an ongoing basis. At Enceiba, we can do this for you.

In fact, you may want to consider a different fulfillment method than FBA. FBA isn't always the right fit for every SKU. Heavy or bulky items often make more sense fulfilled another way, as the size-tier fee structure punishes them under FBA.

4. Get into Amazon’s Bulk Buying Programs

Amazon’s B2B bulk and large-quantity purchase programs are worth a look if you're not already in one. Spreading fulfillment costs across a larger order size makes the per-unit economics better. If your products fit this model, it's one of the more direct ways to offset rising FBA costs without touching price or fulfillment method.

The Bottom Line

Rising FBA fees aren't going away. Manufacturers who protect their margins on Amazon will be the ones who make the most of the platform and perform best over time.

Not sure where your Amazon program stands on any of this? Let's talk. We can analyze your Amazon program and show you exactly where your margin is leaking. And what to do about it.