Fulfillment by Amazon (FBA) has revolutionized the way online sellers operate their businesses. It takes the hassle out of logistics by storing your products, handling packing and shipping, and even managing customer service. However, while the system is convenient, a lot is hidden behind the shiny surface, especially in 2025, when fee changes are catching many sellers off guard.
Understanding the real cost of using FBA means digging into the fine print and planning proactively. This guide walks you through the lesser-known FBA charges that can quietly drain your profits—and how you can stay one step ahead with smart tools and strategies.
Storage Fees: The Silent Expense That Grows With Time
When you use Amazon FBA, you’re paying for more than just warehouse space. You’re essentially renting space in Amazon’s massive fulfillment centers. But in 2025, this rent comes with higher penalties if you don’t manage your inventory wisely.
Let’s say you’re selling Bluetooth speakers. You send 1,000 units to FBA in July, expecting they’ll sell out by the holidays. But by December, only 400 had sold. The remaining 600 units are now subject to long-term storage fees, and this is where it gets expensive.
Amazon divides storage fees into two parts:
- Monthly storage fees – Charged per cubic foot, with higher rates in peak seasons (October–December).
- Aged inventory surcharges – Charged on items stored for more than 180 days.
Here’s the 2025 breakdown:
- 181–270 days: $1.50 per cubic foot
- 271–365 days: $3.80 per cubic foot
- 365+ days: $6.90 per unit, not just space used.
So, if you have 300 units sitting for 9 months, and each unit takes up 0.5 cubic feet:
- Storage fee = 300 × $3.80 × 0.5 = $570 just for holding those items
Now imagine this happening across 5-10 SKUs. That’s thousands lost each quarter.
Why does this matter?
Many sellers focus on sending inventory to FBA but don’t track how long it’s been sitting. The longer it stays, the more it costs—especially when the fees jump from per-cubic-foot to per-unit pricing after 365 days.
Real Solution:
Utilize inventory tools like RestockPro or any age-tracking system to monitor the age of each SKU. Plan flash sales, bundles, or discounts to clear older stock more quickly. You could also consider Fulfilled by Merchant (FBM) for slower sellers to avoid storage fees entirely.
In short, knowing how long your products sit at Amazon is not optional—it’s essential to staying profitable.
Inbound Placement Fees: The Cost of Convenience
Shipping products to Amazon isn’t as simple as it seems. You might think, “I’ll send 500 units to Amazon, and they’ll take care of the rest.” But what most sellers don’t realize is that Amazon often splits your shipment across different warehouses around the country—and charges you for the privilege.
These extra charges are referred to as Inbound Placement Service Fees, and they can silently increase your cost per unit.
Here’s how it works:
Imagine you’re sending in a batch of kitchen blenders. You box them all up and create a shipment in Seller Central. Amazon might decide that 200 units need to go to a warehouse in Texas, another 150 to California, and the remaining 150 to New Jersey. That’s three separate shipments—more packaging, more freight cost, and now: placement service fees.
In 2025, these fees range from $0.27 to $1.58 per unit, depending on size and weight. So if your blender weighs 8 lbs and falls in the higher fee bracket, you’re looking at:
- 500 units × $1.58 = $790 in additional inbound fees for just one shipment!
Now, imagine doing this monthly or with heavier products—your profit can shrink fast without you even noticing.
Why Does Amazon Do This?
Amazon wants to keep products close to customers for faster shipping. So it distributes your items across warehouses near high-demand regions. Suitable for the customer, but costly for you.
What Can You Do?
Use Amazon’s Inventory Placement Service (IPS) if you want to ship all items to a single location, although this option incurs its flat fee. These tools help you configure the box contents smartly so you avoid shipment splits and reduce these hidden fees.
Another trick: Group products by fulfillment region or use prep centers that are closer to Amazon’s high-demand hubs.
Inbound fees may not show up clearly until you’re deep into the shipping process, but they impact your bottom line. Staying aware of them and planning smarter shipping strategies can easily save hundreds or even thousands of dollars each year.
Returns: The Real Cost Beyond Customer Satisfaction
Returns are a normal part of doing business online, especially on Amazon, where the return policy is extremely buyer-friendly. While that’s great for customers, it can be a costly headache for sellers.
Let’s say you’re selling wireless headphones priced at $35. A customer buys them, uses them for a week, and then returns them. You think, “Okay, I’ll just resell them.” But in most cases, you can’t.
Here’s why:
- Amazon’s returns processing fee for 2025 ranges between $2.12 and $6.85 per unit, depending on the product category.
- Returned items may be labeled “unsellable” even if they appear new. If the packaging is opened or the item shows slight wear, Amazon often marks it for disposal or return-to-seller, both of which come with extra fees.
- On top of that, you might not get back the full referral fee you initially paid to Amazon. In some cases, Amazon refunds the buyer the full amount, while keeping a portion of the fees.
Imagine getting 100 returns in a month. Even at the lower end of the processing fee scale ($2.12), that’s $212 lost, not counting the value of lost inventory or removal and disposal fees.
How to Reduce the Damage:
Start by analyzing your return reports in Amazon Seller Central. Are people returning because of size issues? Misleading photos? Product malfunctions?
If you sell clothes or shoes, returns are common due to fit problems. Make your size charts clear, offer photos showing how the item fits different body types, or even link to customer reviews that mention fit.
Also, use feedback monitoring tools like FeedbackWhiz to track review trends. If you see patterns like “didn’t match the description” or “came broken,” take action—update your product images, add protective packaging, or rewrite unclear copy.
Returns don’t just affect profit—they impact your account health too. Too many returns can lead to listing suspension or lower seller ratings. The key is to prevent returns before they happen and be strategic when they do.
Unplanned Service Fees: Penalties for Non-Compliance
Unplanned Service Fees are Amazon’s way of penalizing sellers for sending inventory that isn’t prepped correctly. These fees can seem small per unit, but quickly snowball if you’re not careful, especially if you’re dealing with hundreds or thousands of units.
Let’s say you sell ceramic mugs. You sent 500 mugs to FBA without proper packaging. Amazon checks the shipment and notices that each mug lacks bubble wrap. Since mugs are fragile, they need to be protected individually. So, Amazon wraps them for you—but charges you a per-unit prep fee, which can range from $1.00 to $2.20 per item, depending on the task.
That’s an unexpected charge of up to $1,100 just for one batch of mugs.
Common Triggers of Unplanned Fees:
- Missing or incorrect barcodes: Amazon can’t identify your product without a proper FNSKU barcode. They’ll apply it for you—for a fee.
- Insufficient packaging: Items that need bagging, taping, or wrapping and are not prepped properly will be handled by Amazon and charged.
- Mislabeled boxes: Incorrect carton details can delay processing and lead to manual corrections at a cost.
Why It Hurts:
Not only do these fees cost you money, but they also delay your inventory from going live, which can result in missed sales, especially during high-traffic seasons like Prime Day or Black Friday.
How to Avoid It:
Follow Amazon’s FBA Prep Requirements carefully. Each product category has specific rules. Print proper barcodes using thermal printers, and if you’re using third-party prep services, ensure they’re Amazon-compliant.
You can also use tools like the Print Transparency Barcode feature to label inventory accurately. This helps ensure your shipments are correct before they even leave your warehouse.
In short, a small mistake in prep can lead to big losses. Pay attention to the details upfront—it’ll save you time, money, and frustration later on.
Advertising Wastage: Not a Fee, But a Profit Leak
Advertising waste isn’t listed on your Amazon FBA fee report, but it can drain your profits faster than any visible cost. Think of it as money slipping through your fingers—dollars spent on ads that don’t convert into sales.
Imagine you’re selling phone cases. You run Sponsored Product ads with a daily budget of $50. Your Advertising Cost of Sale (ACoS) creeps up to 45%, meaning you’re spending $0.45 to earn every $1 in revenue. That might not seem bad until you realize your profit margin is only 30%. You’re losing money with every sale.
Here’s what contributes to ad waste:
- High ACoS: If your cost to advertise exceeds your profit margin, every sale is a loss.
- Ads running during low-conversion hours: If your ads run at 2 AM when no one’s shopping, your budget is being wasted.
- Targeting broad or irrelevant keywords: Keywords like “phone accessories” are expensive and vague. You’ll burn through your budget fast with few actual buyers.
Say you spend $1,500 on ads in a month. If $500 of that is spent on poorly timed or mis-targeted ads, that’s $500 lost—money that could’ve gone to profitable campaigns or inventory.
What’s the Fix?
Use dayparting tools to schedule ads only during high-conversion hours (e.g., 8 AM–10 PM in your target market). Also, review your search term reports weekly. Cut keywords with high spend and low sales, and double down on those bringing profitable conversions.
If you’re not using tools, even Amazon’s free “Campaign Manager” has performance data.
Bottom line: It’s not about spending more on ads—it’s about spending smarter.
Removal and Disposal Fees: A Pricey Exit Plan
One of the most painful and often unexpected costs of selling on Amazon is what happens to inventory that doesn’t sell or arrives defective. You can’t just let it sit there because Amazon will charge you long-term storage fees. But removing or disposing of it? That’s not free either.
In 2025, Amazon raised removal fees by 20%, meaning you now pay more just to get your products back. If a unit previously cost $0.50 to remove, it could now cost $0.60 or more, depending on size and weight.
Let’s say you have 1,000 units of a product that didn’t perform well. Maybe it got poor reviews, or it’s seasonal and missed its sales window. Now it’s just sitting in a fulfillment center, aging and costing you money daily.
You decide to remove 500 units:
- Removal cost (average): $0.60 × 500 = $300
- Plus, you’ve already paid for monthly storage and possibly long-term storage.
- If you dispose of them instead? Still costs per unit—sometimes more if it requires special handling.
The worst part? That product is no longer bringing in any revenue. You’re spending money just to make it go away.
How to Avoid It:
- Forecast smarter: Don’t send 2,000 units if you’ve only sold 300 in the past 3 months. Use tools that track sales velocity and suggest optimal reorder quantities.
- Liquidate early: If a product is underperforming, consider offering discounts, Lightning Deals, or Amazon Outlet pricing before fees accumulate.
- Monitor inventory age: The older your inventory, the more it costs to hold or remove. Track it weekly, not just quarterly.
Using tools like Seller Labs’ Restock App or Inventory Health reports can help flag SKUs that need attention before they become liabilities.
Moral of the story: Sending products to Amazon is easy. Getting them out? Not so much—and it’ll cost you if you’re not careful.
Refund Adjustments and Restocking Fees: The Hidden Deductions
Securing a sale on Amazon may seem like a win, but what happens when the customer requests a refund? Many sellers think that once a product is returned, the entire process resets with no cost to them. Unfortunately, that’s not true. Amazon often makes deductions behind the scenes that quietly eat into your profits, and these can be more damaging than you realize.
Let’s say you sell a massage gun for $60. The customer returns it after one week. Amazon issues a full refund to the buyer, but you don’t get all your money back.
Here’s what could be deducted:
- Referral Fee (Amazon’s commission): You may lose this completely or partially.
- Restocking Fee: Amazon charges the customer a fee for returning the product, but it doesn’t always refund that amount to you.
- Return Processing Fee: If the item is in a category such as electronics or apparel, you may be charged between $2.12 and $6.85 for the return to be processed.
- Unsellable Product: If the product is damaged or opened, Amazon may label it as “unsellable,” meaning you will either need to pay for removal or disposal.
Now multiply that by 20 returns in a month, and you’ve silently lost hundreds of dollars, especially with mid- to high-ticket items.
How to Protect Your Margins:
- Review Return Reports weekly in Seller Central.
- Use tools like FeedbackWhiz or Helium 10’s Refund Genie to analyze return reasons and automate refund claims when Amazon misses reimbursements.
- Keep product descriptions, photos, and sizing charts clear and concise to minimize confusion.
- Communicate post-sale with customers using tools like ZonGuru to prevent misunderstandings that lead to returns.
- For high-value items, consider adding tamper-proof packaging to reduce return fraud.
Returns are part of eCommerce, but the goal should always be to reduce them, understand why they happen, and recover what you’re owed.
2025 Fee Changes: What’s New and What You Must Know
Each year, Amazon revises its FBA fee structure, and 2025 introduced several important updates that are already affecting seller margins. If you’re not paying close attention, you could be underpricing your products or missing out on opportunities to adapt.
Let’s look at the significant changes:
1. Dimensional Weight Pricing Expanded
Amazon now calculates fees based not only on actual weight but also on package dimensions. That means a lightweight but bulky product like a pillow could now be charged as if it weighs 5 times more than it does.
For example:
- A 1 lb throw pillow in a 20x20x10 inch box could be charged as 4 or 5 lbs dimensional weight, drastically increasing your fulfillment fees.
2. Holiday Peak Surcharges
If you sell a product during Q4 (October to December), be ready to pay higher storage and fulfillment fees. Amazon introduced peak season fees to offset its higher operational costs. This impacts sellers who rely heavily on holiday sales and don’t plan.
3. Changes to Small and Light Program
This program, designed to help sellers offer affordable, lightweight items with lower fees, has seen revised thresholds for size, weight, and pricing. If your product used to qualify and no longer does, your fulfillment costs may rise significantly.
What You Can Do:
- Recalculate profit margins regularly using tools like Jungle Scout’s Profit Calculator or AMZScout.
- Use InventoryLab to simulate fee scenarios and model your profit under the new fee structure.
- Consider using packaging optimization services or consulting 3PLs to rework your shipping materials and reduce dimensional weight charges.
- Always review Amazon’s fee update at the start of each quarter and adjust your pricing, bundling, and promotional strategies accordingly.
Being reactive to fee changes can cost you. But staying proactive keeps your business agile, competitive, and profitable—even when Amazon moves the goalposts.
Need Expert Help? eMarspro Can Guide You Through the FBA Maze
eMarspro is a full-service eCommerce agency specializing in Amazon consulting, PPC campaign management, and complete account optimization. Our team works closely with sellers to reduce operational inefficiencies, manage advertising budgets, and uncover hidden profit drains you might not even realize exist.
Reach out to eMarspro today and let us help you protect your margins, grow your brand, and take the guesswork out of selling on Amazon.
