Manual vs. Automated Shopify Backorder Management: Which System Fits Your Store?

When a Shopify store oversells by 50 units because of a manual backorder process, the fallout is immediate: lost revenue, angry customers, and hours of cleanup.

Many merchants believe backorder management means choosing between lost sales and operational chaos.

This guide compares manual and automated Shopify backorder management strategies, so you can capture every sale, protect customer trust, and scale without sacrificing your team’s sanity.

What Shopify backorders really cost your store

Shopify backorders can be a growth lever or a liability. Your management approach determines whether you capture sales or lose customers and revenue.

When Brand Z’s manual backorder system failed during Black Friday, they lost $75,000 and 500 customers in a single weekend. This is not a rare event. Every time a customer clicks “buy” on an out-of-stock item, your backorder process faces a critical test. Get it right, and you capture sales that competitors miss.

Get it wrong, and you face refund requests, negative reviews, and accounting headaches that ripple through your business for weeks.

Shopify’s “continue selling when out of stock” feature allows customers to purchase items even when inventory hits zero. The system marks these orders as backorders in your admin panel and continues accepting payments while you restock.

Unlike pre-orders, where customers expect a wait, backorders often catch buyers by surprise. They expect normal fulfillment times and are frustrated by delays.

The real costs of mismanaged backorders include:

• Overselling and refund processing
• Delayed fulfillment and increased cancellations
• Customer support overload
• Accounting reconciliation delays

If you sell on Shopify, Amazon, and eBay, inventory mismatches multiply your risk. One delayed sync can trigger an avalanche of overselling and weeks of cleanup.

Now, let us break down what manual Shopify backorder management really looks like and where it breaks down as you scale.

Manual Shopify backorder management: Risks, hidden costs, and when it works

Manual management starts simply. You enable “continue selling when out of stock” in Shopify, update product pages with restock dates, and track orders in spreadsheets. For a handful of orders, this feels manageable. As you scale, the cracks appear fast.

Here is what manual Shopify backorder management actually demands:

• Daily inventory checks across all sales channels
• Manual customer notifications for each backorder
• Spreadsheet updates tracking order status and restock dates
• Individual refund processing when customers cancel
• Manual reconciliation between Shopify orders and accounting software
• Constant monitoring to prevent overselling across channels

These financial impacts translate directly into time costs that compound as you scale.

Table 1: Time audit for Shopify backorders

When manual management still makes sense:

• Fewer than 10 SKUs
• Single sales channel (Shopify only)
• Low order volume (under 100 per month)
• Direct owner oversight

But even in these cases, manual management creates a growth ceiling. These systems scale only to about 1,000 orders per month, and beyond that, you become a data-entry team.

Here is how ecommerce automation changes the game.

3 automation categories that eliminate 90% of backorder headaches

Automated backorder solutions, like Webgility’s inventory sync, order/accounting platforms, and warehouse integrations, reduce errors, save time, and scale with your business.

Understanding these failure points reveals exactly where automation can eliminate the most painful bottlenecks. There are three main categories:

1. Inventory sync tools

• Keep stock levels accurate across channels in real time
• Best for: Stores with 10-500 SKUs, 1-3 channels, simple ecommerce accounting
• Setup: 2 hours; Cost: $75-$300/month

2. Order/accounting platforms

• Integrate order management, inventory sync, and accounting
• Best for: Multi-channel sellers using QuickBooks or Xero
• Setup: 5 days; Cost: $300-$1,000/month

3. Warehouse/3PL integrations

• Manage fulfillment across multiple warehouses or 3PLs
• Best for: Retailers with complex fulfillment or multiple locations
• Setup: 4 weeks; Cost: $1,000+/month

Platforms like Webgility integrate order management, inventory sync, and accounting, so when a backorder is fulfilled, your QuickBooks entry, inventory cycle count, and customer notification all update automatically.

Ready to set up your system? Here is how to do it step by step.

Setting up Shopify backorders: Manual and automated step-by-step

Whether you manage backorders manually or with automation, setting up Shopify correctly is the foundation for success.

Manual setup

• In Shopify admin, go to the product, scroll to Inventory, and check “Track quantity”
• Enable “Continue selling when out of stock”
• For products with variants, enable this setting for each variant as needed
• Update product descriptions or banners to set customer expectations (“Available on backorder, ships in 2 weeks”)
• Edit order confirmation emails to mention possible backorders

Shopify does not offer conditional email logic for backorders, but you can add a general note to confirmation emails. For more advanced notifications, use a backorder app or inventory tool.

Decision framework: Which Shopify backorder system fits your store?

Your best-fit Shopify backorder system depends on order volume, channel complexity, and accounting needs. Use this quiz to find your answer.

Quick quiz:

1. How many SKUs do you manage?
2. How many sales channels do you sell on?
3. How often do you run out of stock?
4. Do you use QuickBooks or Xero?
5. What is your team size?

Score bands:

• Low (Manual is fine): <10 SKUs, 1 channel, rare stockouts, no accounting integration, solo operator
• Mid (Inventory sync tool): 10-100 SKUs, 2–3 channels, occasional stockouts, basic accounting, small team
• High (Full automation): 100+ SKUs, 3+ channels, frequent stockouts, QuickBooks/Xero, growing team

Migration path checklist:

• Audit your current manual process
• Set up your chosen tool
• Run in parallel for 2 weeks
• Go live with inventory management automation
• Review results monthly

Once you have chosen your system, use these best practices to optimize results.

Your 30-day roadmap to Shopify backorder automation (Best practices and advanced strategies)

Optimize your Shopify backorder process with clear communication, regular reviews, and data-driven forecasting.

Best practices for all:

• Proactive customer communication (e.g., “Your item is on backorder and will ship by [date]”)
• Regular inventory audits to catch discrepancies early
• Monitor backorder rates and cancellation trends

For automation users:

• Configure exception alerts for low-stock or delayed orders
• Use analytics for SKU-level forecasting
• Review automation rules monthly to ensure accuracy

Advanced strategies:

• Use demand forecasting to minimize backorders
• Set reorder points at 2x average daily sales
• Run ABC analysis to prioritize high-impact SKUs

Webgility’s analytics dashboard helps you track Shopify backorder trends and forecast demand with confidence.

It syncs inventory in real time across Shopify, Amazon, eBay, POS systems, and QuickBooks. The platform automatically updates on hand and available quantities as orders come in, preventing the mismatches that lead to backorders and oversells.

The Wine Cellerage, a wine retailer managing inventory between their online store and QuickBooks Enterprise, struggled with manual inventory updates that left their storefront showing inaccurate stock levels.

After implementing Webgility, they gained real-time inventory visibility, saved at least 10 hours per week on manual data entry, and kept their online store accurate without constant manual adjustments.

Book a demo with Webgility today.

Frequently asked questions (FAQs)

How can I keep customers informed about backorders?

You can update order confirmation emails to mention possible backorders. Automation tools like Webgility can also trigger notifications when backordered items ship.

Can I choose which products allow backorders on Shopify?

Yes, you can enable “continue selling when out of stock” only for selected products or variants in your Shopify admin.

What is the main difference between a backorder and a pre-order?

Pre-orders are for items not yet released, so customers expect a wait. Backorders are for out-of-stock items that will be restocked soon.

Will automation help with customer messaging for backorders?

Yes, platforms like Webgility can automate customer notifications for order status, shipping updates, and backorder alerts.