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Key Takeaways
In e-commerce, unpaid invoices are different from those in traditional B2B: they include transactions declined in real time, expired cards, and subscriptions that aren’t renewed. These losses often go unnoticed because there are no invoices sitting in a drawer to serve as a reminder. Three scenarios come up regularly: subscription dunning, deferred-payment B2B invoices, and pending disputes. For each of these, platforms (Shopify, WooCommerce, Stripe) offer native modules. The real issue isn’t the tool itself, but rather the seamless integration between the online store, the payment solution, the CRM, and the ERP—the very area where IT Systèmes supports small and medium-sized businesses.
In traditional B2B, an unpaid invoice is obvious: an invoice has been issued, the due date has passed, and a reminder needs to be sent. In e-commerce, it’s more subtle. The payment fails at the time of the transaction; the customer doesn’t always notice it, and neither does the company if the information isn’t flagged. A card expires, a spending limit is exceeded, or a subscription renewal fails. No one has forgotten anything, and yet the money doesn’t come through.
These losses often go unnoticed because there are no invoices lying around in a drawer to remind us of them. This is one of the classic blind spots of an IT system that has been built up in successive layers—a topic we discuss in greater detail in our article on business digitization.
This guide covers the three most common scenarios and how to handle them automatically, whether your store runs on Shopify, WooCommerce, Stripe, or uses deferred B2B billing.
Three Types of Unpaid Invoices Specific to E-Commerce
Dunning: Failed Subscription Payments
Dunning is the automated management of declined payments on a recurring basis. Whether it’s an expired card, an exceeded credit limit, or a bank decline—with every failed transaction, a customer may leave without even intending to, simply because no one notified them that their payment method was no longer valid.
The rule can be summed up in one sentence: Respond quickly with a direct link to update the map. No justification, no explanatory paragraph. One link, one action.
B2B Invoices with Deferred Payment
Some stores sell to businesses with 30- or 60-day payment terms. The e-commerce platform generates the invoice, but it cannot manage a phased collection process over time. You’ll need to connect the store to accounting software (Pennylane, Sage, Sellsy) or an automation tool (Make, Power Automate) via API. These invoices then follow the same process as a standard B2B collection procedure: a friendly reminder, a firm reminder, and a formal notice.
Pending Disputes and Refunds
A customer is disputing a transaction or is waiting for a credit that hasn’t been issued yet. Sending them a payment reminder in this situation is the surest way to turn a complaint into a chargeback. The system must recognize these statuses and remove the affected transactions from the reminder process. This requires reliable synchronization with the payment platform, and that’s precisely where things get complicated when the integration is poorly implemented.
Setup based on your platform
On Shopify. Failed subscription payments are handled natively through Shopify Payments and Shopify Subscriptions. For advanced features (SMS, segmentation by customer value, integration with CRM), Klaviyo or ActiveCampaign integrate directly with Shopify payment events.
On WooCommerce. WooCommerce Subscriptions handles recurring payments and automatic retries in case of failure. AutomateWoo then lets you create conditional rules directly from WordPress: stop reminders once payment is received, tailor the message based on the number of attempts, and exclude customers with disputed orders. For common scenarios, no custom development is required.
For a subscription-based model, Stripe Billing and Chargebee include basic dunning features: retries according to a configurable schedule, an email sent with each attempt, and conditional suspension of service. For simple subscriptions, Stripe Billing is sufficient. For more complex scenarios (multi-currency, B2B dunning, advanced CRM integration), Chargebee or Recurly offer more flexibility.
For a B2B store with deferred billing. The platform generates the invoice but does not manage staggered reminders. The solution is to connect the store to your accounting software or to Make/Power Automate. The workflow retrieves open invoices, monitors due dates, and triggers reminders based on your scenarios.
Here is a sample workflow for failed payments, which you can adapt to suit your business:
What Really Makes a Difference in the Results
The timing of the first follow-up is more important than anything else. As long as the purchase is still fresh in the customer's mind, updating their card information takes just a few seconds. A few days later, that intention has faded.
The call-to-action link must be direct. A button that takes users to the payment method update page—not to the home page or the general customer portal. Every extra click results in lost customers.
Automatic termination is not a minor detail. As soon as the payment is processed, the sequence must stop. A reminder sent after payment has been made creates more problems than it solves and damages the customer relationship.
The limit on the number of attempts also matters. After a few reminders, the effort doesn't yield much of a return and eventually becomes annoying. Knowing when to stop is part of the process.
Finally, just a little personalization is enough: first name, the product in question, and the exact amount. There’s no need to say more than necessary.
Integration: The Real Technical Issue
Choosing the right tool is rarely the hard part. The real challenge lies in integrating the e-commerce platform, the payment solution, the CRM, and the ERP. A poorly configured workflow leads to exactly what we wanted to avoid: reminders sent after payment, duplicate entries, or gaps in coverage for certain customer segments.
For an SME or mid-sized company, this integration work often involves an existing information system, with its own constraints and history. That’s where IT Systèmes comes in: auditing existing workflows and setting up connections between the online store, payment systems, and internal tools—particularly in Shopify, WooCommerce, Stripe, and Microsoft 365 environments. This type of project falls within our expertise in development and automation, where the challenge lies less in writing code and more in ensuring that tools that don’t natively communicate with each other can interact seamlessly.
Frequently asked questions
Is Stripe Billing sufficient for managing collections for a subscription-based store? For simple subscriptions, yes. Stripe Billing offers configurable dunning with automatic retries and collection emails. For more complex scenarios (multi-currency, B2B collections, advanced CRM integration), Chargebee or Recurly provide greater flexibility.
Can you automate follow-ups on WooCommerce without any coding? Yes, with WooCommerce Subscriptions and AutomateWoo. These plugins let you set up follow-up sequences from within WordPress—without writing any code—for most common scenarios.
How can you avoid sending a reminder to a customer who has already paid? By synchronizing the payment status in real time with the reminder tool. On Stripe or Shopify, payment webhooks allow you to stop a sequence in just a few seconds. On less responsive systems, such as an ERP with daily reconciliation, including a grace period in the triggers reduces the risk.
Do you need a different tool for B2B and for subscriptions? Not necessarily, but the processes differ. Subscriptions involve dunning (card retry), while deferred B2B payments involve invoice follow-up (staggered reminders). Many companies use both systems side by side: a dunning module on the payment side and a workflow linked to the accounting software on the billing side.
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