Is it possible to manually capture deferred payments for Shopify pre-orders with variable shipping costs?

Many Shopify merchants want to collect pre-order deposits now, but only capture the final deferred payment (including updated shipping costs) when products are actually ready to ship. While this sounds straightforward, manually capturing variable deferred payments requires a complex Shopify workflow that goes beyond what most standard pre-order apps, including Early Bird, currently support.

In this article we explain why manual payment capture with variable shipping is challenging on Shopify, what are the existing workarounds, and what alternatives you can consider for your pre-order strategy.

Why manual deferred payment capture with variable shipping costs is complex on Shopify

Most Shopify pre-order systems, including Early Bird, work with:

• Fixed Shopify payment dates set in advance
• Static product information from when the pre-order was placed
• Pre-determined final payment amounts that customers agree to upfront

What merchants looking for variable shipping pre-orders usually need:

• Manual trigger control over when Shopify deferred payments are processed
• Dynamic shipping cost recalculation based on updated product info or shipping dates
• Ability to process different SKUs at different times when they become available on Shopify
• Variable final payment amounts that customers haven't pre-approved

The core challenge: Shopify doesn't natively support dynamic pricing for deferred payments yet, because it's difficult to get customers to agree to pay an unknown future amount through Shopify's payment system.

Yes, Shopify supports manual payment capture, but with important limitations for this type of pre-order scenario. You can set up manual capture to authorise payments at checkout and capture them later when ready to fulfill. However, you can only capture up to the originally authorised amount - you cannot collect additional fees like variable shipping costs that weren't included in the initial authorisation.

For pre-orders with variable shipping, you'd need to either estimate shipping costs upfront and include them in the authorisation, or use separate invoicing for additional charges after the initial payment capture.

Potential Shopify workarounds for manual payment capture

If you need to attempt this variable shipping pre-order workflow on Shopify, here are some approaches, though each has major limitations:

Option 1: Capture Deposit via Early Bird + Manual Invoicing (If you have a high volume of orders)

Shopify setup:

• Set initial deposit in your Early Bird pre-order campaign to product cost minus estimated shipping
• Configure Shopify shipping profiles for $0 shipping cost on pre-orders
• Plan to manually invoice remaining amounts through Shopify when products are ready

Shopify process:

1. Customer pays deposit through your Early Bird pre-order campaign setup
2. When product is ready, manually adjust the order (Shopify has now enabled editing orders containing items with a fixed selling plan, but still with many restrictions)
3. Send invoice via Shopify Orders Admin for the remaining balance including actual shipping
4. Manually fulfill the Shopify order after final payment is received

Limitations:

• Customers may be surprised by final invoice amounts
• There's no guarantee customers will pay the second invoice
• Difficult to communicate final costs clearly upfront
• This manual process isn't scalable
• Customers can be easily confused about total costs

Additional things you should be aware of:

• When you send invoice via Shopify Orders Admin, customers must complete a full checkout process, not just pay a simple invoice
• The deferred payment system requires customers to go through checkout again with billing info and shipping method selection
• If multiple products in a pre-order have different payment due dates, all payments will be due on the earliest date
• Early Bird will handle the deposit collection for you, but the final payment collection through Shopify's deferred payment system is a separate checkout experience
• The "manual invoicing" is actually sending customers to complete checkout, which adds friction to the customer experience

Option 2: Modify Early Bird Shopify orders before payment dates (If you don't have a high volume of orders)

Shopify setup:

• Use Early Bird and list the estimated final/deferred payment amounts in your pre-order campaign
• Set deferred payment dates far in the future in your pre-order campaign
• Plan to manually adjust Shopify orders before the automatic capture date arrives

Shopify process:

1. Customer completes pre-order with estimated amounts through Early Bird
2. Before the automatic payment date, manually edit orders in Shopify admin
3. Update shipping costs and final amounts in Shopify
4. Allow Early Bird to process the updated amounts through Shopify

Limitations:

• Must remember to update every order before the deferred payment dates
• Risk of automatic processing with the wrong amounts if you forget to edit
• You can only adjust amounts downward from the original authorisation
• Time-sensitive manual intervention required
• Still requires customer agreement to variable pricing upfront

Recommended alternatives for complex Shopify pre-order workflows

Custom Shopify development solution

If you're a Shopify brand that needs this level of pre-order complexity, a custom-built Shopify solution might be more suitable, even if it requires significant development time and cost. This could include:

• A custom Shopify solution for pre-orders
• Integration with external payment processing beyond Shopify's native options
• Dynamic pricing calculations for Shopify pre-orders
• Manual trigger controls for Shopify payment processing

Shopify Plus Partner agencies for complex pre-orders

We spoke to trusted Shopify Plus Partner agencies before (not affiliated in any way) who specialise in complex Shopify e-commerce workflows. They can help assess whether custom Shopify development is worth the investment for your pre-order needs or if any workarounds not mentioned here exist.

Get in touch with us if you'd like recommendations for Shopify Plus Partner agencies we trust for your complex pre-order implementations.

Alternative Shopify business models for variable shipping

Consider whether adjusting your Shopify business model might achieve similar pre-order goals:

• Estimated shipping with Shopify refunds: Charge estimated shipping upfront through Shopify, refund differences
• Shipping ranges in Shopify: Provide shipping cost ranges customers agree to in Shopify checkout
• Free shipping thresholds: Build shipping into Shopify product costs
• Regional Shopify pricing: Set different prices by shipping zones in Shopify

Communication is crucial for any Shopify pre-order workaround

If you proceed with manual invoicing approaches on Shopify:

Essential Shopify customer communications:

• Clear explanation that final costs may vary in your Shopify pre-order
• Estimated ranges for shipping and total costs in Shopify checkout
• Timeline for when final invoices will be sent through Shopify
• Agreement to pay variable final amounts beyond the initial Shopify payment

Consider adding to Shopify product pages: "Final shipping costs will be calculated when your pre-order is ready to ship based on current rates and your location. You'll receive a final invoice through Shopify before shipping."

When to consider Early Bird vs custom Shopify solutions for pre-orders

Early Bird works well for Shopify pre-orders with:

• Fixed or predictable final amounts in Shopify
• Automated Shopify payment processing
• Standard Shopify shipping calculations
• Scalable Shopify pre-order workflows

Custom Shopify solutions are better for pre-orders with:

• Variable final amounts beyond Shopify's native capabilities
• Manual payment timing control outside standard Shopify flows
• Complex shipping calculations not supported by Shopify
• Unique business requirements beyond standard Shopify pre-order functionality

Need help?

If you're considering a complex pre-order workflow, we recommend first reaching out to discuss whether Early Bird can be adapted to your needs, or if a custom solution would be more appropriate.

Feel free to email us at support@shopside.com.au to discuss your specific requirements (otherwise we're happy refer you to a trusted Shopify Plus agency)!

Last updated on May 30, 2025