Using the Bank Deposit Payment Method on Shopify

Table of Contents

1. Introduction
2. Understanding Manual Payments on Shopify
3. Phase 1: Foundations First
4. Phase 2: Clarify the "Why"
5. Phase 3: Risk and Integrity Check
6. Phase 4: Setting Up the Bank Deposit Payment Method on Shopify
7. Phase 5: Optimize with Intention (The Cartly Pro Approach)
8. Managing the Workflow: After the Order is Placed
9. Performance and Measurement
10. When to Bring in Professional Help
11. Optimization: What Cart/Checkout Tools Can and Cannot Do
12. Conclusion
13. FAQ

Introduction

Have you ever looked at your Shopify analytics and noticed a pattern of customers reaching the final payment step only to vanish? While many merchants immediately assume the price was too high or shipping was too expensive, the reality is often more subtle: the customer simply didn’t see a payment method they trusted or felt comfortable using. Not everyone wants to put a high-value purchase on a credit card, and in many global markets, bank transfers are the preferred way to do business.

The bank deposit payment method on Shopify offers a bridge for these customers. It is what we call a "manual payment method," meaning the transaction doesn’t happen instantly through an automated gateway. Instead, the customer places the order, you provide instructions, and they send the funds through their banking portal. Once the money hits your account, you manually approve the order for fulfillment.

This post is designed for Shopify merchants—ranging from new store owners to established B2B (business-to-business) brands—who want to expand their payment options without introducing unnecessary complexity. We will explore how to set up these methods, when they make sense for your business model, and how to manage the unique risks they carry.

At Cartly Pro, we believe that every element of your checkout—including manual payments—should be part of a deliberate strategy. We call this "Optimizing with Intention." This means focusing on foundations first, clarifying your goals, conducting a risk check, implementing minimal effective changes, and constantly reassessing your data. By the end of this article, you will know exactly how to integrate bank deposits into your customer journey in a way that builds trust and reduces friction.

Understanding Manual Payments on Shopify

Before diving into the setup, it is important to understand what a "manual payment" actually is in the Shopify ecosystem. Unlike Shopify Payments or PayPal, where a successful transaction immediately marks an order as "Paid," a manual payment method puts the order in a "Pending" or "Unpaid" state.

Common manual payment types include:

• Bank Deposits: Direct transfers from one bank account to another.
• Money Orders: A printed order for a pre-specified sum of money.
• Cash on Delivery (COD): Payment collected by the courier upon delivery.
• Custom Methods: Anything from "Pay in Store" to niche local transfer services.

For the merchant, this creates a two-step process. First, the customer commits to the purchase. Second, the merchant must verify the receipt of funds before the order is fulfilled. While this adds a layer of administrative work, it opens doors to customers who are credit-averse or those making massive purchases where credit card limits might be an issue.

Phase 1: Foundations First

At Cartly Pro, we often say that apps and custom payment methods are not the starting line. They are supportive tools within a larger system. Before you decide to activate the bank deposit payment method on Shopify, you must ensure your store’s foundations are solid.

If your core shopping experience is broken, adding a new payment method won't fix it. Check these areas first:

Product-Market Fit and Trust Signals

Does your store look trustworthy? Customers are inherently more cautious when using a manual bank deposit because they lack the "chargeback" protection offered by credit card companies. If your site has low-resolution images, no About Us page, or missing contact information, a customer is unlikely to send a bank transfer to a stranger.

Transparent Policies

Your shipping and return policies must be crystal clear, and your Help Center should answer the same questions. When a customer pays via bank deposit, they need to know exactly how long it takes for you to verify the payment and when their shipping clock actually starts. Transparency is the best way to reduce "where is my order?" emails.

Site Speed and Mobile UX

A slow site creates anxiety. If a customer is already nervous about a manual payment, a lagging checkout page might be the final push they need to abandon the cart. Ensure your theme is optimized and your mobile experience is seamless.

Foundations Check: If your mobile traffic is high but your "Reached Checkout" metric is low, the issue is likely on your product pages or cart experience, not your payment methods. Fix the friction there before adding complex payment options.

Phase 2: Clarify the "Why"

Why are you considering bank deposits? To optimize with intention, you must define what success looks like. Without a clear goal, you risk adding manual labor for your team with no real return on investment.

Scenario A: High-Value B2B Orders

If you sell industrial equipment or wholesale supplies, orders might reach $5,000 or $50,000. Many credit cards have daily limits, and the transaction fees on a $50,000 credit card swipe can be thousands of dollars. In this case, a bank deposit is a logical tool to increase Average Order Value (AOV)—the average dollar amount a customer spends per transaction—by making large purchases easier and cheaper. If this sounds like your business, our case studies can give you a practical benchmark.

Scenario B: International Expansion

In countries like Germany, the Netherlands, or parts of Southeast Asia, bank transfers (like SEPA or local equivalents) are often more popular than credit cards. If you are seeing high abandonment from a specific geographic region, adding a manual bank deposit option can help you capture that market.

Scenario C: Reducing Transaction Fees

Credit card processors typically charge 2.9% + $0.30 per transaction. Bank deposits, while requiring more manual effort to verify, effectively bypass these processing fees (though your bank may charge a small incoming wire fee).

What to do next:

• Identify the specific customer segment that needs bank deposits.
• Estimate the number of manual orders you can realistically handle each week.
• Set a benchmark for success (e.g., "We want to see a 5% increase in checkout completion for B2B customers").

Phase 3: Risk and Integrity Check

Every payment method comes with risks. With credit cards, the risk is usually fraud or chargebacks. With bank deposits, the risk shifts toward "zombie orders" and administrative overhead.

The Problem of Zombie Orders

A "zombie order" occurs when a customer selects "Bank Deposit" at checkout, the inventory is reserved, but the customer never actually sends the money. If you have limited stock, this can be disastrous. Your system thinks the item is sold, so it shows "Out of Stock" to paying customers, while the item sits in your warehouse waiting for a payment that never arrives.

Privacy and Compliance

When providing bank deposit instructions, you are often sharing your business’s account number and routing number. While this is standard in B2B transactions, ensure you are comfortable with this information being visible on the order confirmation page.

Integrity in Communication

Never use "dark patterns"—manipulative design choices—to nudge people toward bank deposits just to save yourself on fees. If you offer a bank deposit, be honest about the delay. It will take 1–3 business days for the funds to clear. If you promise "Next Day Delivery" but don't mention that the clock only starts after the deposit clears, you are damaging your brand's integrity.

Risk Tip: If you have high-demand, low-stock items, consider using an app or a custom rule to disable manual payments for those specific products to prevent inventory hoarding.

Phase 4: Setting Up the Bank Deposit Payment Method on Shopify

Once you have done your homework, it is time to implement. Shopify provides two main paths for manual payments: suggested methods and custom methods.

Using a Suggested Manual Payment Method

Shopify has a built-in "Bank Deposit" option that is pre-configured.

1. From your Shopify Admin, go to Settings > Payments.
2. In the Payment providers section, look for Manual payment methods.
3. Select Bank Deposit from the list.
4. Additional details: Enter information the customer sees during checkout (e.g., "You will receive our bank details on the next page to complete your transfer").
5. Payment instructions: This is the most important part. This info appears on the Order Confirmation page and in the confirmation email. Include your Bank Name, Account Name, Account Number, and Routing/IBAN/Swift code.
6. Click Activate.

Creating a Custom Manual Payment Method

If "Bank Deposit" doesn't sound right for your brand—maybe you want to call it "Secure Wire Transfer" or "Corporate Invoice"—you can create a custom version.

1. In the same Manual payment methods section, select Create custom payment method.
2. Name the method: Be clear. Avoid vague names like "Other." Note that Shopify reserves names like "Bank Deposit" and "Cash," so choose something unique like "Direct Bank Transfer."
3. Provide Instructions: Be explicit. Tell the customer to include their Order Number as the reference for the transfer so you can easily match the payment to the order.

What to do next:

• Place a test order using the bank deposit method.
• Check the order confirmation email to ensure the instructions are easy to read on a mobile device.
• Draft a "Payment Received" email template to send to customers once you've verified their deposit.

Phase 5: Optimize with Intention (The Cartly Pro Approach)

Simply turning on the payment method is the "minimum effective" step. To truly optimize, you need to look at the entire shopping journey. At Cartly Pro, we focus on the "Cart Experience"—the space between the product page and the checkout. If you want to strengthen that layer, install Cartly on your Shopify store.

Reducing Friction in the Cart Drawer

The "Cart Drawer" (the window that slides out when someone adds an item) is a high-leverage moment. If you are targeting B2B customers who prefer bank deposits, you can use the cart drawer experience to set expectations early.

Instead of letting the customer discover the bank deposit option only at the very end of checkout, you could use a small announcement or a "Progress Bar" in the cart drawer that says: "Large order? We accept Direct Bank Transfers for your convenience." This reduces the "What if my card is declined?" anxiety before it even starts.

Clarity via Cart Widgets

You can use sticky add-to-cart widgets to provide a "Request a Quote" or "Pay by Invoice" button that sits alongside the standard "Checkout" button. This allows you to funnel specific customers into the manual payment flow without cluttering the UI for your standard retail customers.

One Change at a Time

Don't overhaul your entire checkout overnight. If you add bank deposits, wait two weeks. Look at your conversion rate—the percentage of visitors who complete a purchase—and your cart abandonment rate. If abandonment goes down but your "Unpaid Orders" list grows too long, you might need to refine your instructions or add a countdown timer to your manual payment orders.

Managing the Workflow: After the Order is Placed

The real work of the bank deposit payment method on Shopify starts after the "Buy" button is clicked.

Monitoring Pending Orders

On your Orders page, these sales will appear with a status of Payment Pending. You should check your business bank account daily. When a deposit arrives, match it to the order number provided in the reference field.

Marking as Paid

Once the funds are confirmed:

1. Open the order in Shopify.
2. Click Collect Payment.
3. Select Mark as Paid.
4. This moves the order to Paid and Unfulfilled, triggering your standard shipping workflow.

When to Cancel

If a customer hasn't sent funds within 48–72 hours, reach out with a friendly reminder. If there is still no response after 5 days, it is usually best to cancel the order and restock the items. This keeps your inventory accurate and prevents "dead" stock from sitting in your system.

Red Flag Guidance: If you notice a sudden influx of large "Bank Deposit" orders from suspicious email addresses, do not fulfill them until the funds are 100% cleared and verified by your bank. If you suspect fraud or account compromise, contact Shopify Support and your payment provider immediately.

Performance and Measurement

You cannot improve what you do not measure. To see if bank deposits are helping or hurting your store, track these metrics in your Shopify Analytics:

• Checkout Completion Rate: Has this improved since adding manual payments?
• Average Order Value (AOV): Are people using bank deposits for larger-than-average orders?
• Payment Lag Time: What is the average number of days between an order being placed and the payment being marked as "Paid"? If this is too long (e.g., over 7 days), your instructions might be confusing.
• Manual Labor Cost: Track how much time your team spends verifying bank deposits. If the time spent exceeds the transaction fees you saved, you may need to reconsider the strategy or set a minimum order value for bank deposits.

Mobile-First Considerations

Most shoppers are on mobile. Bank deposit instructions often involve long strings of numbers (IBANs, Account Numbers). Ensure your instructions are easy to "copy and paste" on a smartphone. Avoid putting your bank details inside an image; keep them as text so the customer can easily move the data to their banking app.

When to Bring in Professional Help

While Shopify makes manual payments relatively simple, there are times when you should consult an expert.

• Custom Code/Theme Issues: If you want to show or hide the bank deposit option based on specific items in the cart, you may need a Shopify developer to help with "Payment Customizations" or apps that use the Shopify Functions API.
• Legal and Tax Compliance: If you are selling internationally, receiving direct bank transfers may have different tax implications or reporting requirements. Always consult a qualified accountant or tax professional when setting up new international payment flows.
• Security Concerns: If you believe your Shopify Admin has been accessed by unauthorized users who might have changed your bank deposit instructions to their own accounts, secure your account immediately and contact Shopify Support.

Optimization: What Cart/Checkout Tools Can and Cannot Do

It is tempting to think that a better cart drawer or a new payment method will solve all your sales problems. Let’s be realistic about what optimization tools (like Cartly Pro) can do for you.

What they CAN do:

• Reduce Friction: Make it easier for the customer to understand their options and move to the next step.
• Increase Clarity: Use announcements and bars to explain shipping, returns, and payment methods before the customer gets frustrated.
• Support Upsells: Offer relevant add-ons in the cart with our upselling and cross-selling guide so the suggestion feels helpful rather than pushy.
• Improve Mobile UX: Ensure buttons and info are perfectly placed for thumb-tapping.

What they CANNOT do:

• Fix Product-Market Fit: If no one wants your product, a better cart won't help.
• Guarantee Revenue: Results depend on your niche, your traffic quality, and your pricing.
• Replace Reliable Fulfillment: No payment method matters if you can't get the product to the customer on time.

Conclusion

Integrating the bank deposit payment method on Shopify is a powerful way to serve B2B clients, international shoppers, and high-AOV customers. However, it is not a "set it and forget it" feature. It requires a commitment to manual verification and a high level of transparency with your customers.

By following the "Optimize with Intention" path, you ensure that your store remains professional, trustworthy, and efficient. For one concrete example, review the Lace Lab case study.

Key Takeaways for Merchants:

• Foundations First: Ensure your site is fast, trustworthy, and mobile-friendly before adding manual payments.
• Goal Clarity: Use bank deposits to solve a specific problem, like high transaction fees on large orders or local market preferences.
• Integrity Check: Be honest about processing times and don't let manual orders clog up your inventory.
• Minimal Implementation: Start with the built-in Shopify manual payment settings and clear instructions.
• Reassess: Monitor your "Unpaid Orders" list and conversion rates to ensure the method is actually helping your business.

At the end of the day, commerce is about trust. Providing a bank deposit option tells your customer: "We understand your needs, and we're willing to work with you." When implemented with care and a focus on clean UX, it can be the final piece of the puzzle that turns a hesitant visitor into a loyal customer.

Ready to improve your store's journey? Start by looking at your cart experience. A better cart today leads to a more confident checkout tomorrow. If you're looking for ways to make your cart experience more informative and conversion-friendly, try Cartly on your Shopify store.

FAQ

How do I mark an order as paid after a bank deposit?

Once you verify the funds in your business bank account, go to the Orders page in your Shopify Admin. Click on the specific order number, select the Collect Payment button, and choose Mark as Paid. This will update the order status and allow you to begin the fulfillment process.

Does Shopify charge transaction fees on bank deposits?

Shopify does not charge its standard transaction fees on manual payment methods like bank deposits. However, keep in mind that your own bank might charge a fee for receiving wire transfers or international deposits. You should check with your financial institution to understand their fee structure.

Is the bank deposit method available on Shopify Mobile?

Yes, you can set up and manage manual payment methods through the Shopify mobile app. Go to Settings > Payments within the app to activate or deactivate manual methods. You can also mark orders as paid directly from your smartphone once you see the funds in your bank account.

How can I prevent customers from forgetting to pay?

Clear communication is key. Use the Payment Instructions field in Shopify to provide a step-by-step guide. Include your bank details and ask the customer to use their Order Number as the transfer reference. Additionally, consider sending a follow-up email 24 hours after the order is placed if the funds haven't arrived.