MerchantFlow Payment Methods Guide

MerchantFlow Payment Methods Guide

MerchantFlow payment methods are managed through your workspace's billing provider. Standard web signups use Stripe-hosted checkout for secure payment processing, while Shopify App Store installs handle payments through the Shopify billing system.

How Payment Works for Stripe-Billed Workspaces

Standard web signups use Stripe-hosted checkout.

During Onboarding

For a new web workspace:

1. The owner reaches /onboarding/payment
2. Selects a tier (Starter, Pro, or Plus) and a billing cadence (monthly or annual)
3. Optionally applies a referral or coupon code
4. Clicks Start 14-Day Free Trial
5. MerchantFlow creates a Stripe checkout session
6. Stripe collects the payment method on its hosted page

MerchantFlow requires a verified email before the Stripe checkout session can be created. Subscriptions are denominated in USD.

After Onboarding

From Settings > Billing:

• When a card is on file, the Payment Methods card shows its brand, last four digits, and expiry, with an Update Card button that opens the Stripe billing portal
• Add Payment Method is shown when the workspace does not yet have a card on file - during a trial it appears with the date you need to add one by

Stripe handles the payment form and billing portal UI. MerchantFlow does not expose raw card storage inside the app.

Important Limits

• Demo accounts cannot open the live Stripe billing portal
• Shopify-billed tenants cannot use Stripe payment management for that workspace

How Payment Works for Shopify-Billed Workspaces

Shopify App Store installs use Shopify billing.

• Plan approval happens in Shopify
• Payment methods are managed on the Shopify side
• Charges appear with the rest of your Shopify bill

Shopify-Billed Workspaces Only Show Relevant Controls

MerchantFlow detects when a workspace is Shopify-billed and hides irrelevant payment-method controls and invoice listings from the in-app billing page. You will not see Stripe-specific actions ("Update Card", "Open Stripe Portal") or Stripe invoice rows for a Shopify-billed tenant - those would never apply. Instead you will see a link out to Settings > Billing in Shopify admin, which is the source of truth for payment methods and invoices on this path.

This keeps the billing page focused on what you can actually do, and prevents accidental clicks that would lead to an empty Stripe portal.

How to Change Your Payment Details

Use the control that matches your billing provider:

• Stripe tenants are routed through Stripe checkout or the Stripe billing portal
• Shopify tenants update payment details in Shopify admin

Troubleshooting Payment Issues

"Billing says I need to verify my email"

That is expected on the Stripe path. MerchantFlow blocks checkout creation until the owner's email is verified. Check your inbox for the verification email or visit Security for details.

"Billing sent me to the wrong provider"

The billing provider is fixed at the tenant level:

• Standard web signup uses Stripe
• Shopify App Store install uses Shopify

If the tenant was created through Shopify, use the Shopify billing path even if you can also sign into MerchantFlow directly.

"Update Card is unavailable"

This usually means one of the following:

• The workspace is a demo or development-only billing state (the button is disabled for demo workspaces)
• The tenant is Shopify-billed, so the Payment Methods card is hidden entirely
• Stripe customer setup has not been completed yet

"My payment failed - how long do I have?"

A failed subscription payment moves the workspace to past due and opens a 21-day grace window during which access continues and MerchantFlow emails you dunning reminders. Update the card from Settings > Billing before the window closes, or access is blocked until payment succeeds.

If you are unsure which path your workspace uses, check Billing Overview or contact [email protected].

Frequently Asked Questions

What payment methods does MerchantFlow accept?

For Stripe-billed workspaces, MerchantFlow accepts payment methods supported by Stripe checkout, including major credit and debit cards. Shopify-billed workspaces use whatever payment methods are configured in your Shopify account.

How do I update my credit card in MerchantFlow?

Go to Settings > Billing and click Update Card to open the Stripe billing portal. If the button is unavailable, check that your workspace uses Stripe billing and that checkout has been completed.

Is my payment information stored securely?

Yes. MerchantFlow does not store raw card data. All payment processing is handled by Stripe (for web signups) or Shopify (for App Store installs), both of which are PCI-DSS compliant.

Why can't I add a payment method to my MerchantFlow workspace?

This may happen if your email is not verified, the workspace is in demo mode, or the workspace uses Shopify billing. Verify your email first, then retry from Settings > Billing.

Can I use PayPal to pay for MerchantFlow?

Payment method availability depends on your billing provider. Check with Stripe or Shopify for their supported payment methods.

Related Pages

• Pricing Plans
• Trial Period
• Invoices

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Last updated: August 23, 2026