Connecting Shopify to Shipsidekick: Integration Guide

Understanding the Shipsidekick-Shopify Integration

The connection between Shipsidekick and Shopify creates a seamless flow of information between your online store and warehouse operations. When integrated properly, orders flow automatically from Shopify to your fulfillment system, inventory updates push back to your store in real-time, and customers receive tracking information without any manual data entry.

Shipsidekick's native Shopify integration is built specifically for ecommerce fulfillment, handling the complexities of multi-location inventory, product variants, and order management that generic integrations often struggle with.

Two Ways to Connect

Shipsidekick provides two convenient methods to establish the Shopify connection, giving you flexibility based on your preferences and workflow.

Connecting Through Shipsidekick

The first method is connecting directly within Shipsidekick. Navigate to Integrations & Connections from the main menu and select Shopify from the available integrations. You'll be prompted to enter your Shopify store URL and authorize the connection.

This method works well when you're setting up Shipsidekick for the first time or adding a new Shopify store to an existing Shipsidekick account. The connection process takes just a few minutes and immediately establishes the data flow between systems.

Connecting Through the Shopify App Store

Alternatively, you can install the Shipsidekick app directly from the Shopify App Store. Search for "Shipsidekick" in the Shopify apps section, click install, and follow the authorization prompts. This method connects your store to Shipsidekick through Shopify's app marketplace.

Many users prefer this approach because it's familiar if you've installed other Shopify apps, and it provides easy access to the integration settings from within your Shopify admin panel. Both connection methods establish the same integration functionality, so choose whichever workflow feels more comfortable.

How the Integration Works

Once connected, Shipsidekick and Shopify communicate through webhooks, which are real-time notifications that trigger whenever specific events occur. This webhook-based approach ensures information flows immediately without polling delays or batch updates.

Real-Time Order Detection

When a customer places an order on your Shopify store, Shopify immediately sends a webhook notification to Shipsidekick. Within 30 seconds to a couple of minutes, that order appears in your Shipsidekick dashboard ready for fulfillment.

This near-instant order detection means your warehouse team can begin picking and packing orders almost immediately after customers complete checkout. There's no waiting for hourly batch imports or manual order syncing. The speed advantage is significant for businesses promising same-day or next-day shipping.

The webhook system also captures order changes. If a customer modifies their order before it ships, or if you edit an order in Shopify, those changes flow to Shipsidekick automatically. This synchronization prevents situations where you ship the wrong items because the order changed after initial import.

Product and Inventory Synchronization

Product information syncs in both directions between Shopify and Shipsidekick, keeping your catalog and inventory accurate across both systems.

When you add a new product in Shopify, the webhook notification triggers and Shipsidekick creates the corresponding product record within minutes. Product details like title, SKU, variants, weight, and dimensions all transfer automatically. This instant product sync means you can list new products in Shopify without separately creating them in your warehouse system.

Product updates work the same way. Change a product title, add a new variant, or update product weight in Shopify, and those changes appear in Shipsidekick automatically. This bidirectional sync eliminates the tedious work of maintaining product catalogs in multiple systems.

Inventory Updates Push to Shopify

Inventory accuracy is critical for ecommerce success. Overselling products you don't have creates customer disappointment and refund requests. Shipsidekick pushes inventory changes to Shopify as soon as they occur, ensuring your store displays accurate stock levels at all times.

When you receive inventory in Shipsidekick, the quantity increase pushes to Shopify immediately. When you ship an order, the inventory decrease updates Shopify in real-time. If you conduct a cycle count and adjust quantities, those adjustments sync to Shopify within seconds.

This instant inventory synchronization means your Shopify store never shows products as available when they're actually out of stock. Customers see accurate availability, and you avoid the operational headaches and customer service issues that come from overselling.

Shipment Information Returns to Shopify

After you pack an order and generate a shipping label in Shipsidekick, the shipment information automatically flows back to Shopify. This includes the tracking number, carrier, shipping method, and items shipped.

Shopify then triggers its fulfillment notifications to customers, sending tracking information via email. The order status in Shopify updates to fulfilled, and the tracking number appears in the customer's order history. This automation eliminates the manual process of updating order status and entering tracking numbers in Shopify.

For partial shipments where you ship some items before others, Shipsidekick communicates the partial fulfillment to Shopify with tracking for the shipped items. The order remains partially fulfilled in Shopify until all items ship, maintaining accurate order status throughout the fulfillment process.

Configuring Integration Settings

The Shipsidekick-Shopify integration includes several configuration options that give you control over how the systems communicate.

Warehouse-to-Location Mapping

If you manage multiple warehouses in Shipsidekick, you can map each warehouse to specific Shopify locations. Shopify's location feature allows stores to track inventory across multiple fulfillment centers, retail stores, or warehouses.

In Shipsidekick, configure which warehouse corresponds to each Shopify location. This mapping ensures inventory from your Los Angeles warehouse updates the correct Shopify location, while inventory in your New York warehouse updates its corresponding Shopify location.

Proper warehouse-to-location mapping is essential for accurate inventory display on your storefront. If a customer in California visits your site, Shopify can show them products available from your Los Angeles warehouse for faster shipping. The integration maintains this location-specific accuracy automatically once configured.

For single-warehouse operations, this configuration is straightforward: map your one Shipsidekick warehouse to your primary Shopify location. For multi-warehouse 3PLs managing inventory for multiple clients, carefully configure location mappings for each client to maintain inventory separation.

Inventory Push Controls

Shipsidekick provides a control to enable or disable inventory pushes to Shopify. This toggle is particularly useful during initial setup when you're loading inventory data into the warehouse management system.

When setting up a new store connection, you typically want to disable inventory pushes initially. This prevents Shipsidekick from updating Shopify inventory while you're still receiving products, counting stock, and establishing accurate baseline inventory in the WMS.

Once your inventory data in Shipsidekick is accurate and matches your actual physical stock, enable inventory pushes. From that point forward, every inventory change in Shipsidekick automatically updates Shopify, maintaining synchronization.

You might also temporarily disable inventory pushes during major inventory corrections, physical inventory counts, or data migrations where you're making bulk changes that shouldn't immediately affect your live store. After completing the corrections, re-enable pushes to resume automatic synchronization.

This control gives you confidence that you won't accidentally zero out inventory on your live Shopify store while setting up or troubleshooting your warehouse system.

Setting Up the Integration

Proper setup ensures smooth operation from day one and prevents common integration issues.

Before You Connect

Before connecting Shopify to Shipsidekick, complete several preparation steps that make the integration process smoother.

Ensure your product SKUs in Shopify are accurate and unique. The SKU is the primary identifier linking products between systems. Products without SKUs or with duplicate SKUs create matching problems that cause fulfillment errors.

Review your Shopify locations if you use multiple warehouses. Verify that locations are configured correctly in Shopify before connecting to Shipsidekick, as you'll be mapping Shipsidekick warehouses to these locations.

Note your current Shopify inventory levels. You'll want to compare these against inventory in Shipsidekick after the initial sync to verify everything matched correctly.

Decide on your inventory management approach. Will Shipsidekick be the source of truth for inventory, or will you manage inventory in both systems? Best practice is making Shipsidekick the inventory authority and letting it push accurate counts to Shopify.

The Connection Process

Navigate to Integrations & Connections in Shipsidekick (or the Shopify App Store) and initiate the Shopify connection. You'll be redirected to Shopify to authorize Shipsidekick's access to your store data.

Shopify displays the permissions Shipsidekick requests, including read and write access to orders, products, and inventory. Review these permissions and click authorize to grant access. These permissions are necessary for the integration to function and are standard for fulfillment system integrations.

After authorization, you're redirected back to Shipsidekick where you'll configure the integration settings. Map your Shipsidekick warehouse to the appropriate Shopify location. If you have multiple warehouses, create mappings for each one.

Decide whether to enable inventory pushes immediately or keep them disabled during setup. For new implementations, start with pushes disabled while you establish accurate baseline inventory.

Initial Data Sync

Once connected, Shipsidekick begins syncing existing data from Shopify. All products, variants, and orders import from Shopify into Shipsidekick. This initial sync might take several minutes to an hour depending on how many products and orders exist in your Shopify store.

Monitor the initial sync to ensure products are importing correctly. Check that SKUs, titles, and variants match between systems. Verify that existing unfulfilled orders appear in Shipsidekick's order list.

If you notice issues during the initial sync, such as products not matching correctly or orders missing, address them before proceeding. Common issues include SKU mismatches, products without SKUs, or connectivity problems. Shipsidekick's support team can help troubleshoot sync issues if needed.

Verifying the Integration

After the initial sync completes, test the integration to confirm bidirectional communication is working properly.

Create a test order in Shopify and verify it appears in Shipsidekick within a couple of minutes. This confirms order webhooks are functioning correctly.

Add a new product in Shopify and check that it appears in Shipsidekick. This verifies product sync is working.

If you've enabled inventory pushes, make a small inventory adjustment in Shipsidekick and verify the change appears in Shopify. This confirms inventory synchronization is functioning.

Process a test order completely through Shipsidekick, generating a shipping label and marking it shipped. Verify that the order updates to fulfilled in Shopify with tracking information visible. This end-to-end test confirms the entire fulfillment workflow is integrated properly.

Best Practices for Managing the Integration

Once your integration is running, follow these practices to maintain smooth operations.

Keep SKUs Consistent

SKUs are the glue holding the integration together. They must match exactly between Shopify and Shipsidekick. Any mismatch creates orphaned products that won't sync properly.

When adding new products, use the same SKU in both systems. If you create a product in Shopify first, it syncs to Shipsidekick with the Shopify SKU. If you create products in Shipsidekick first, use those exact SKUs when creating products in Shopify.

Never change a SKU in one system without changing it in the other. SKU changes break the link between product records and create duplicate or orphaned products. If you must change a SKU, plan a coordinated change in both systems or reconnect the integration to resync products.

Monitor Sync Status

Periodically verify that the integration is syncing properly. Check that recent orders appear in Shipsidekick, that inventory levels match between systems, and that shipments are updating Shopify correctly.

Most sync issues are obvious because orders stop appearing or inventory becomes inaccurate. If you notice discrepancies, investigate immediately rather than letting them accumulate. Small sync problems become major headaches if ignored.

Handle Disconnections Properly

Occasionally, integrations disconnect due to API changes, authorization expirations, or connectivity issues. If your Shopify integration disconnects, Shipsidekick alerts you to the problem.

Reconnect as soon as possible to resume automatic data flow. While disconnected, orders won't import automatically and inventory won't sync. The longer the disconnection persists, the more manual reconciliation you'll need to do.

After reconnecting, verify that orders placed during the disconnection imported correctly and that inventory levels synchronized properly. You may need to manually import orders or adjust inventory if the disconnection lasted more than a few hours.

Communicate Integration Status to Your Team

Ensure your team knows that Shopify and Shipsidekick are integrated and understands what that means for their workflow. They should know that orders appear automatically, inventory updates push automatically, and shipments sync tracking information back to customers.

Team members shouldn't manually create orders in Shipsidekick that already exist in Shopify, as this creates duplicates. They shouldn't manually adjust inventory in Shopify when the adjustment should happen in Shipsidekick. Clear communication about the integration prevents duplicate work and data conflicts.

Use Shipsidekick as Inventory Authority

With the integration active, make Shipsidekick your source of truth for inventory levels. Conduct receiving, adjustments, and cycle counts in Shipsidekick, letting those changes push to Shopify automatically.

Avoid making inventory adjustments directly in Shopify, as this can create discrepancies if the adjustment doesn't sync back to Shipsidekick. When inventory in your warehouse changes, record that change in your warehouse system (Shipsidekick), not in your sales channel (Shopify).

This approach maintains a clear data flow direction and prevents conflicts where both systems are trying to be authoritative about inventory levels.

Troubleshooting Common Issues

Understanding common integration issues and their solutions helps you resolve problems quickly.

Orders Not Appearing in Shipsidekick

If Shopify orders aren't appearing in Shipsidekick, first verify the integration is still connected. Check the integration status in Shipsidekick's Integrations & Connections area.

Confirm that the orders are actually placed and not just abandoned carts. Only completed orders with payment sync to Shipsidekick, not draft orders or carts.

Check if the orders are assigned to a Shopify location that's not mapped to a Shipsidekick warehouse. Unmapped orders won't import because Shipsidekick doesn't know which warehouse should fulfill them.

Inventory Not Syncing to Shopify

If inventory changes in Shipsidekick aren't appearing in Shopify, verify that inventory pushes are enabled in the integration settings. This is the most common cause of inventory sync issues.

Confirm that the warehouse containing the inventory is properly mapped to a Shopify location. Inventory in unmapped warehouses won't push to Shopify because there's no destination location.

Check that the products have matching SKUs between systems. If SKUs don't match, Shipsidekick can't identify which Shopify product to update with inventory changes.

Tracking Numbers Not Appearing in Shopify

If you're shipping orders but tracking numbers aren't appearing in Shopify, verify that you're completing the shipment properly in Shipsidekick. Simply printing a label doesn't trigger the fulfillment notification; you must mark the order as shipped.

Confirm that the carrier used in Shipsidekick maps to a carrier that Shopify recognizes. Shopify supports specific carrier names for tracking display, so custom carrier names might not format correctly.

Duplicate Products or Orders

Duplicate products typically occur when a product exists in both systems with different SKUs, then the integration creates a new product during sync rather than matching the existing one. Fix duplicates by ensuring SKUs match, then removing the duplicate records.

Duplicate orders can happen if someone manually creates an order in Shipsidekick that already imported from Shopify. Train team members to check whether an order exists before manually creating it.

Benefits of the Native Integration

Shipsidekick's native Shopify integration provides advantages over generic middleware or manual processes.

The real-time webhook-based communication ensures immediate data flow without delays. Orders, products, and inventory changes sync within seconds or minutes, not hours. This speed enables faster fulfillment and more accurate inventory display.

The integration is built specifically for ecommerce fulfillment workflows, handling product variants, multi-location inventory, and partial shipments correctly. Generic integrations often struggle with these complexities.

Native integration eliminates the cost and complexity of third-party middleware platforms. You don't need Zapier, Shopify Flow, or custom API development to connect your store and warehouse system.

The direct connection is more reliable than multi-step integrations with additional failure points. Fewer moving parts means fewer things that can break.

The Bottom Line

Connecting Shopify to Shipsidekick through the native integration creates a powerful automated fulfillment system where orders flow from customers to your warehouse instantly, inventory remains accurate across both systems, and tracking information reaches customers automatically. The webhook-based real-time communication ensures data is always current, while configuration options like warehouse-to-location mapping and inventory push controls give you the flexibility to tailor the integration to your specific operational needs. Taking time to set up the integration properly, maintaining consistent SKUs, and following best practices for managing the connection ensures smooth operations that scale with your business growth. When Shopify and Shipsidekick work together seamlessly, you spend less time on data entry and more time shipping orders and growing your business.