Organizely connects to Shopify so your catalog, inventory, and orders stay aligned without manual re-keying. This page walks you through connecting your store, running the first import, and keeping everything in sync afterward.
Before you begin
Setting up and configuring integrations requires Manager or Admin access.
The modern way to connect is by installing Organizely from the Shopify App Store. Installing the app creates the connection for you and lets Shopify manage the webhooks that keep data flowing (there is no per-store webhook setup to do). Older, manually connected stores still work, but new stores should use the App Store install.
Connect your Shopify store
Install the Organizely app from the Shopify App Store and approve the requested permissions.
Follow the prompts to hand off into the main Organizely app.
Once connected, your Shopify store appears under Integrations → Manage. Open it to see its detail page, with tabs for Details, Products, Settings, Webhook Logs, Inventory Sync Logs, and Health.
Note: For App Store installs, webhooks are managed centrally by Shopify, so the manual "Initialize Webhooks" action is not needed (it is disabled for these stores).
Run the first import (Initialize Integration)
The first time you connect, run a one-time setup that pulls your Shopify data into Organizely.
Go to Integrations → Manage and open your Shopify integration.
In the Actions card, click Initialize Integration.
Leave the page to work in the background. A "Processing..." badge and an "Operations in Progress" list show each step live (indexing products, importing your products, then importing your order history).
What initialization does:
Prepares the connection and its sync configuration (and, for manually connected stores, its webhooks).
Reads and indexes your Shopify products.
Imports and creates your products in Organizely.
Imports your order history.
Warms up your analytics once the data is in.
Note: Large catalogs and long order histories can take a while. The import runs as a background job, so you can close the page. Organizely emails you when initialization finishes.
Tip: Wait for the initial import to complete before you manually create products or orders in Organizely. Letting Shopify import cleanly first avoids duplicates and mismatches.
If your store has a very large order history, the first import brings in a large batch and shows how many were imported. To bring in the rest of your history, contact support.
After the import: real-time, two-way inventory sync
Once initialization is complete, your Shopify data is fully available and inventory stays in sync automatically.
Inventory syncs bidirectionally in real time. A stock change in Shopify updates Organizely, and inventory movements in Organizely (such as goods receipts, stock adjustments, and stocktake commits) sync back to Shopify.
New orders flow in from Shopify automatically as webhooks arrive.
You control the direction and scope of sync on the integration's Settings tab, which is split into Inbound Sync (Shopify to Organizely) and Outbound Sync (Organizely to Shopify), each with per-resource toggles for products, variants, inventory, and more. You can also override these settings at the product or variant level.
Note: Outbound sync writes changes back into your Shopify store. Review what each toggle does before enabling it.
Product mapping and SKU matching
The Products tab on the integration lists your Shopify products and how they map to Organizely. You can search by product, variant, or SKU there.
Variants are matched by SKU, so keeping SKUs consistent between the two systems keeps the mapping clean.
If two Shopify variants share one SKU, that duplicate-SKU conflict is surfaced on the Health tab. The affected variant stays connected without a SKU and keeps syncing inventory and orders; the issue resolves automatically once the SKU is fixed in Shopify or Organizely.
Manual sync triggers
Most syncing happens automatically, but the integration's Advanced Options card gives you manual controls for one-off or catch-up runs:
Initialize Webhooks: set up webhooks for a manually connected store (disabled for App Store installs, where Shopify manages webhooks centrally).
Index Products: re-read products from Shopify (a prerequisite for imports).
Import All Products: import, create, and sync your products from Shopify.
Import All Orders: import, create, and sync your orders from Shopify.
Sync Locations: pull your Shopify store locations into Organizely.
Resync Committed from Shopify: force an immediate refresh of committed inventory (units in placed but unfulfilled orders).
To re-run the whole setup, use the Initialize Integration button at the top of the page: once your store is initialized it reads "Re-initialize Integration" and re-runs the setup, which re-initializes webhooks, re-indexes products, and refreshes your sync configuration.
Note: These bulk actions overwrite Organizely with the latest data from Shopify, including products and variants where sync is disabled. Bulk operations do not trigger custom automations, but inventory updates still sync. If you need a more targeted import, contact support.
Monitor and troubleshoot sync
Each integration has tabs to see what is happening and diagnose issues:
Inventory Sync Logs: a record of inventory synchronizations, useful for debugging stock discrepancies.
Webhook Logs: the incoming webhook activity from Shopify.
Health: known recurring sync issues, deduplicated into one entry per problem with an occurrence count, first and last seen times, and a plain-language fix. Issues resolve automatically when the underlying cause is fixed, and you can acknowledge an issue to mark it as known. The Integrations page shows an alert when any issue needs attention.
Need help?
If your Shopify sync is not behaving as expected, reach out to our support team.