Amazon’s Rumored FBA Fee Restructure Is Quietly Splitting Its Biggest Sellers

Something is shifting inside Amazon’s Seller Experience org, and the whispers have grown loud enough that several seven- and eight-figure sellers are already war-gaming contingency plans. According to three sources with direct knowledge of internal Amazon discussions, the company has been quietly piloting a restructured FBA fee framework in select seller cohorts since late Q1 2026 — one that would move away from the current flat dimensional-weight model toward a tiered velocity-based structure that rewards sellers moving more than 500 units per SKU per month.

Amazon has not made any public announcement. The company declined to comment for this story. But sources close to the matter say the internal project, reportedly codenamed “Project Throughput,” has been briefed to at least two of Amazon’s largest third-party logistics partners and may surface as a formal policy update before Q4 2026 peak season begins.

What Is Amazon’s Alleged ‘Project Throughput’ and Who Does It Target?

The alleged restructure, as described by sources, would create three fee tiers based on trailing 90-day unit velocity per parent ASIN. Sellers in the lowest tier — reportedly those moving fewer than 100 units per month per SKU — could see fulfillment fees increase by as much as 12 to 18 percent. Mid-tier sellers, in the 100-to-500 unit range, would see fees remain largely flat. High-velocity sellers above 500 units monthly would reportedly receive a modest reduction of 4 to 7 percent per unit fulfilled.

If accurate, the implications are significant. The current FBA fee structure already layers storage fees, aged-inventory surcharges, and dimensional weight calculations on top of per-unit fulfillment costs. Adding a velocity penalty would compound margin pressure for the exact seller segment — emerging private label brands in the $500K to $3M annual revenue range — that Amazon has historically courted most aggressively through its Launchpad and Brand Registry programs.

“If this is real, Amazon is essentially taxing experimentation. You can’t build velocity before you have velocity. It’s a catch-22 that punishes new SKU launches and rewards incumbents who already have flywheel momentum.” — Jason Somerville, founder of JW Strategic Group and longtime Amazon PPC consultant

💡 Article Summary

Key Insights

1

What Is Amazon’s Alleged ‘Project Throughput’ and Who Does It Target?

2

Which Seller Profiles Stand to Lose the Most Under the New Model?

3

Is This Connected to Amazon’s Push to Consolidate Its Fulfillment Network Efficiency?

4

How Are Major Amazon Seller Tool Vendors Responding Behind the Scenes?

5

What Are Sellers Actually Doing Right Now to Prepare?

Source: Ecommerce Times

Which Seller Profiles Stand to Lose the Most Under the New Model?

The sellers most exposed, according to sources and independent analysis, fall into a few recognizable buckets:

• Wide-catalog private label brands running 50 to 200 SKUs with uneven velocity distribution — a small number of hero ASINs subsidizing dozens of slower tail SKUs. Under the alleged tiered model, those tail SKUs become significantly more expensive to carry in FBA.
• Seasonal sellers in categories like outdoor, holiday décor, and back-to-school, whose velocity naturally collapses for six to eight months per year and would likely fall into the low-tier penalty bracket for much of the calendar.
• New product launchers using the standard 90-day ramp-up strategy popularized by tools like Helium 10’s Cerebro and Jungle Scout’s Opportunity Finder, who would face higher fees during the precise window when margins are already thinnest.
• Supplement and consumable brands with subscription-heavy demand curves that are difficult to predict on a trailing 90-day basis.

Conversely, established brands with concentrated SKU catalogs and predictable reorder cycles — think dominant players in phone accessories, pet supplies, and kitchen tools — would likely benefit from the velocity discount tier.

Is This Connected to Amazon’s Push to Consolidate Its Fulfillment Network Efficiency?

Several supply chain insiders say the timing is not coincidental. Amazon’s North American fulfillment network has been under visible strain since the company’s aggressive warehouse expansion in 2021 and 2022 was followed by a painful contraction phase. The company has been publicly signaling its intent to improve “network utilization” and “cost per unit fulfilled” metrics on quarterly earnings calls throughout 2025 and into 2026.

Unconfirmed reporting from Marketplace Pulse earlier this month noted an uptick in Amazon’s use of inventory placement fees for sellers without the Inventory Placement Service add-on — a move that sources say is related to the same internal efficiency push behind Project Throughput.

“Amazon doesn’t restructure fees in isolation. When you see placement fees tighten and storage surcharges expand at the same time, that’s a coordinated signal. They’re trying to reshape what inventory sits inside their walls.” — Leah McHugh, Amazon policy analyst at ecommerceChris

Sources at two major 3PL operators — one of which counts several hundred Amazon sellers as clients — say they have already begun fielding calls from sellers asking about hybrid FBA/FBM (Fulfilled by Merchant) models as a hedge. One source at a fulfillment center in the Columbus, Ohio metro area said inbound inquiries about Seller Fulfilled Prime eligibility have risen noticeably in the past 60 days, though they attributed some of that to the earlier SFP crackdown coverage rather than Project Throughput specifically.

How Are Major Amazon Seller Tool Vendors Responding Behind the Scenes?

The rumor has reportedly reached the product roadmap discussions at several of the major Amazon seller software platforms. Sources familiar with internal conversations at Helium 10 say the company’s product team has been evaluating whether to add a “fee scenario modeler” to its Profitability Calculator that would allow sellers to simulate outcomes under multiple FBA fee structures. A spokesperson for Helium 10 declined to confirm or deny the feature development, saying only that the company “continuously evaluates enhancements based on seller feedback.”

Jungle Scout, which competes directly with Helium 10 on research and analytics, has reportedly been less reactive internally — though one source described the mood there as “cautious monitoring” rather than active product response. Perpetua, the Amazon PPC automation platform, is allegedly in early discussions about whether velocity-based fee tiers would require recalibrating its bid optimization logic, since ACOS targets are downstream of margin assumptions that the new fees would directly affect.

“Every PPC tool on the market right now prices efficiency against a relatively stable cost base. If fulfillment costs become dynamic based on velocity, you’ve just introduced a variable that makes every existing optimization model less reliable.” — an anonymous product manager at a leading Amazon ad tech platform

What Are Sellers Actually Doing Right Now to Prepare?

Veteran sellers and aggregators who have heard the rumors are already running internal scenarios. At least two Amazon aggregators — neither of which agreed to be named — have reportedly begun auditing their portfolio SKUs against the hypothetical tier thresholds. The playbook being discussed internally at one aggregator includes:

• Identifying tail SKUs with fewer than 80 average monthly units and flagging them for potential FBM migration or outright discontinuation.
• Accelerating PPC spend on mid-tier SKUs that are close to the 500-unit velocity threshold to push them into the lower-fee bracket before any rule changes take effect.
• Opening conversations with 3PL partners about Seller Fulfilled Prime capacity as a backup fulfillment rail for penalized SKUs.
• Re-evaluating minimum order quantities with suppliers to reduce FBA inbound shipment frequency and minimize placement fee exposure.

Brandon Young, founder of Seller Systems and a widely followed voice in the private label community, posted obliquely to his community Slack last week about “fee environment uncertainty” and urged sellers to model their contribution margins at multiple cost-increase scenarios. He declined to comment further for this story, citing the unconfirmed nature of the reports.

When Could Amazon Officially Announce a Fee Change — and What Happens If It Does?

Amazon has historically used its annual fee update cycle — typically announced in late October or November for January implementation — as the vehicle for structural changes. Sources close to the matter say Project Throughput, if it clears internal review, would most likely enter that announcement window, giving sellers a 60- to 90-day runway before implementation.

However, one source cautioned that Amazon has shown willingness to introduce fee changes outside the standard cycle when operational pressures are acute, pointing to the mid-year inbound placement fee adjustments made in 2024 as precedent.

The bigger concern among sellers and aggregators is not the magnitude of any single fee increase but the compounding effect. At a time when Amazon PPC CPCs in competitive categories have risen an estimated 22 percent year-over-year according to internal Perpetua benchmark data, and Category Referral Fees have crept upward across apparel and beauty, even a 12 percent fulfillment fee increase on slow-moving SKUs could tip dozens of ASINs from marginal profitability into sustained losses.

For now, the story remains unconfirmed. But the level of chatter inside Amazon’s seller community — at conferences, in private Slack groups, on the seller forums that Seller Central’s own team reportedly monitors — suggests that where there is smoke, there may well be a fee restructure on its way.

Ecommerce Times will continue to monitor this story. If you have direct knowledge of Amazon’s fee restructuring discussions, contact our editorial team securely.