When you run an online business, chargebacks are just part of the game. But now, Stripe is changing the rules-and not necessarily in your favor.

If you’re using Stripe to process payments, you need to know about their new dispute fee structure and how it could impact your bottom line.

Stripe has always charged a fee when a customer fights a transaction. Now, they’re rolling out new policies that push merchants toward using their AI-powered Smart Disputes tool. If you decide to fight one manually, Stripe will charge you an extra fee. And if you win one using their AI tool, Stripe takes a significant cut of the recovered funds.

Sound complicated? It is. But understanding these changes is important for protecting your revenue and making smart decisions about how you handle disputes.

AVOID CHARGEBACKS AND DISPUTES

The New Stripe Dispute Fee Structure

Starting June 17, 2025, Stripe is doubling down on dispute fees, making it more expensive for merchants to fight chargebacks.

Whenever a customer disputes a transaction, Stripe immediately charges a $15 fee. This fee applies whether you choose to fight it or not and is non-refundable-even if you win the case.

If you decide to challenge the dispute by submitting evidence, Stripe now adds a second fee: a $15 “counter fee.” This means that if you lose the dispute after fighting it, you’ll pay a total of $30: $15 for receiving it and another $15 for responding to it.

The only way to get the counter fee refunded is to win the dispute. However, the original $15 fee remains non-refundable regardless of outcome.

Here’s a quick breakdown of the new structure for U.S. merchants:

• Dispute received: $15 fee (non-refundable)
• Dispute challenged: Additional $15 counter fee (refunded only if you win)
• If you win: You pay $15 (counter fee is returned)
• If you lose: You pay $30 ($15 fee + $15 counter fee)

This change means merchants must be much more strategic about which ones they choose to fight. Fighting all of them can quickly double your costs if you lose, especially if your average transaction size is low.

Stripe’s reasoning is that card networks have increased their own chargeback fees, and the process is resource-intensive for everyone involved.

Ultimately, the new fee structure puts more pressure on merchants to prevent disputes in the first place and to carefully consider the financial risk before contesting a chargeback.

DECREASE CHARGEBACKS, INCREASE CONVERSIONS

Stripe’s Push Toward Smart Disputes (AI Dispute Tool)

Stripe isn’t just changing their fee structure, they’re actively steering merchants toward their new AI-powered solution. Smart Disputes, currently in public preview, is Stripe’s attempt to automate the tedious process of fighting chargebacks.

Smart Disputes uses an AI-powered rules engine to analyze incoming disputes automatically. The system extracts relevant evidence from Stripe’s internal data, your transaction records, and cardholder information to create tailored evidence packets designed to help you win cases.

When you receive an eligible dispute, Stripe notifies you by email and in the Dashboard, and if you don’t take action, the system automatically submits the pre-filled evidence packet before the deadline expires.

The financial incentive to use Smart Disputes is clear: Stripe waives the new $15 counter fee when you use their AI tool. However, this comes with a significant trade-off-if you win using Smart Disputes: Stripe takes a 30% cut of the recovered amount.

This success fee replaces the refunded counter fee model used in manual submissions.

For example, if you successfully recover $100 using Smart Disputes, Stripe keeps $30 of that amount. You’ll still pay the initial $15 fee, but you’ll avoid the counter fee. If it’s lost, you only pay the standard $15 fee, with no counter fee applied.

This approach creates an interesting calculation for merchants. For transactions under $100, Smart Disputes might be cost-effective compared to manual handling. But for higher-value transactions, that 30% success fee can quickly exceed what you’d pay handling them manually.

It’s worth noting that Smart Disputes isn’t guaranteed to work for all cases. Eligibility depends on multiple factors, including the reason code, payment method, and evidence availability. The system also lacks access to external data like your CRM records or customer communications that might be crucial in complex cases.

While Stripe positions Smart Disputes as putting your “disputes on autopilot,” they acknowledge that the final decision still lies with the card issuer. You’re essentially trading control and potentially higher costs for convenience and time savings.

AVOID STRIPE DISPUTES ALTOGETHER

Manual vs. Automated Chargeback Handling: Pros and Cons

When it comes to handling chargebacks, you now face a major decision: manage them manually or let Stripe’s AI handle them. Each approach offers distinct advantages and drawbacks that directly impact your bottom line.

Manual Handling

Pros:

• You maintain complete control over the evidence submitted
• You can include external evidence Stripe’s AI doesn’t have access to
• You pay a fixed fee ($15 + $15 counter fee) regardless of transaction size
• If you win, you keep 100% of the recovered amount (minus the initial $15 fee)
• You can tailor your response to the specific circumstances of each one

Cons:

• You must pay the $15 counter fee upfront (refundable only if you win)
• The process requires significant time and attention from your team
• You need expertise in dispute resolution to maximize win rates
• You face tight deadlines for evidence submission
• If you miss a deadline, you automatically lose

Smart Disputes (AI-Powered)

Pros:

• No upfront counter fee to pay
• Saves significant time and staff resources
• Automatically meets submission deadlines
• Works well for straightforward disputes with standard evidence
• Handles routine disputes without requiring your attention

Cons:

• Stripe takes 30% of any amount you recover
• For high-value transactions, this fee can be substantial
• Limited ability to include external evidence or context
• Less control over how your case is presented
• May not be eligible for all types

When to Choose Each Approach

Consider manual handling when:

• The amount is large (generally over $150)
• You have strong external evidence not available to Stripe
• It involves complex circumstances requiring explanation
• You have expertise in handling chargebacks
• You’re confident in your ability to win the case

Consider Smart Disputes when:

• The amount is relatively small (under $150)
• It’s is straightforward with standard evidence
• You lack the time or resources to handle it manually
• You want to automate the process completely
• You’re dealing with a high volume of low-value disputes

The math becomes clearer with examples: For a $50 chargeback, the 30% success fee ($15) equals the manual counter fee. But for a $500 dispute, the success fee jumps to $150-far exceeding the $15 counter fee you’d pay handling it manually.

Smart Disputes essentially functions as a convenience fee. You’re paying Stripe to handle the process for you. For busy merchants with limited resources, this might be worth it. But for merchants with higher-value transactions or those who already have effective chargeback management processes, manual handling likely remains more cost-effective.

Ultimately, the best approach depends on your business model, average transaction size, chargeback volume, and internal resources. Many merchants will likely adopt a hybrid strategy-using Smart Disputes for lower-value transactions while manually handling higher-value ones where the 30% fee would be excessive.

How We Handle Chargebacks

At DirectPayNet, we don’t charge a counter fee the way Stripe does. This is a cost-saving and merchant-friendly approach, especially for businesses with frequent or high-value disputes.

Let us help you fight chargebacks and avoid disputes altogether. DirectPayNet is here to help you scale.

PREVENT CHARGEBACKS AT THE GATEWAY