Hi everyone, I am trying to improve my store workflow and wanted to ask for advice. What is the best way to keep product inventory accurate when using third party tools or doing manual stock counts? I feel like my available and on hand numbers often don’t match. How do you handle this on your stores?
Hey! This is a super common issue. Shopify inventory gets messy FAST when other tools or manual counting is involved. A few things help keep “available” vs “on hand” from drifting:
1. Pick ONE source of truth for inventory
If your stock is being updated from three different places (Shopify, an app, and someone doing manual counts), the numbers will always fight each other.
Choose one system as the master (usually Shopify) and make every other tool sync from it, not modify it independently.
2. Turn off adjustments in apps that shouldn’t control stock
A lot of people don’t realise that apps like bundling tools, preorder apps, warehouse tools, or dropshipping connectors can all modify inventory.
Check each app’s settings → disable stock adjustments unless it’s literally your inventory tool.
3. Use Shopify Locations properly
If you have multiple locations but put all stock in “default,” it will throw off available/on-hand numbers after transfers or edits.
Make sure:
• each physical/virtual location is set up
• stock is assigned correctly
• transfers are logged (don’t skip this step!)
4. Manual stock counts MUST use “Stocktake” or bulk edit
A lot of people update stock by editing products one by one; that causes mismatches.
Use:
Products → Inventory → Adjust → Reason: Stocktake
This resets the on-hand numbers in a clean, trackable way.
5. If using third-party tools, schedule synced updates
Random syncing = random inaccuracies.
Scheduled syncing = stability.
6. Always check for negative stock
If any app allows selling below 0, your available vs on-hand will NEVER match.
Hi,
Great question this is something a lot of store owners struggle with, especially when using multiple tools or updating stock manually.
Here are a few things that can help keep your inventory accurate and consistent:
Use one system as your “source of truth”
If you’re using a third-party inventory app, make sure it’s the main place updates happen. Any manual edits in Shopify can create mismatches.
Enable inventory sync if using external tools
Most third-party solutions have scheduled sync options (every 5–30 minutes). Using automatic updates reduces human error.
Schedule regular stock audits
Weekly or bi-weekly quick counts and a full monthly inventory check can really help keep the numbers aligned.
Lock stock during counts
If you’re physically counting inventory while orders are still coming in, numbers can shift. Temporarily pausing stock changes during auditing prevents that.
Track transfers and returns properly
These are common causes of differences between “available” and “on hand.”
Use barcode scanning if possible
It makes stock adjustments far more accurate and faster.Everyone’s setup is a little different, but consistency in one workflow usually solves most discrepancies.
Hi @eric18
The best practice is to have a single source of truth for inventory either Shopify or your 3rd party tool and push all updates through it. Routine manual counts should reconcile any differences, and use CSV or API imports for mass updates. Enable “track inventory” by location to avoid overselling on multiple channels.
Hi,
Hope this will help
- Enable Inventory Tracking in Shopify for every SKU
- Use location-based inventory rules
- Some third-party tools push updates instantly and others in batches. Pick tools that sync in real-time
- Barcode scanning for physical counts
- Use audit logs to track all inventory changes
- Limit who can manually adjust numbers
Hi @eric18
The mismatch between “Available” and “On Hand” numbers is a common issue, especially when you start using third-party apps that modify your product data.
You might want to look into an automation tool like Easify Inventory Sync. It focuses specifically on the “syncing” aspect to keep your workflow accurate:
-
Real-time Syncing: It automatically syncs your inventory updates. If a sale happens or you adjust stock manually, it updates the numbers instantly so “Available” always matches reality.
-
Solves the “Product Options” Gap: Most product option apps do not create actual variants in the backend, which means Shopify has nothing to track. Easify fixes this by linking those custom options to your actual inventory, ensuring stock is deducted correctly even for items that aren’t standard variants.
-
Flexible (Single or Multi-Store): It works whether you are managing a single store or need to sync stock across multiple expansion stores later on.
It basically acts as a bridge to ensure your manual counts and app data are always speaking the same language.
Hope that helps fix the discrepancy! Feel free to reach out to Easify in-app live chat if you need any support! 
I keep inventory accurate by using one clear source of truth and making sure no other apps can change stock on their own. All inventory is assigned to the correct Shopify locations and every transfer or return is logged instead of manually editing quantities. When I do manual counts, I only use the Stocktake adjustment so the numbers reset cleanly and stay traceable. I also pause inventory changes during physical counts and never allow negative stock. Since sticking to this workflow, my available and on hand numbers stay in sync.
For us it was fixed when we chose one place as the source of truth. Shopify keeps the stock and all third-party apps only read from it, not modify it. Before that we allowed other tools to adjust quantities and ended up not knowing which number was correct.
Hi @eric18,
Our app, BR Stock Take, can help you keep your inventory counts up to date.
BR Stock Take | Shopify App Store
$15 USD per month with a 15-day free trial.
BR Stock Take uses your manual count and Shopify’s Available, Committed, and Reserved stock to figure out if there are any stock errors in your store. You can manually count your products using the on-screen buttons, use an external barcode scanner, or even use the camera scanner on mobile devices.
You can review all the mismatched products where your Actual manual count does not match the stock reported by Shopify. Once you are done counting all your products, you can click the “Update inventory” button to fix all the stock errors in Shopify.
The app emails you an inventory report with the before-and-after stock, along with a stock valuation, which is super useful for year-end accounting. All your completed stocktakes are available for 2 years within our app, so you can go back and look at your historical inventory data.
Let us know if you have any questions.
Thanks,
support@brdatasolutions.com
BR Data Solutions
Hi,
Actually this happens to a lot of stores — it’s usually because too many tools are changing inventory at the same time.
What’s helped me is keeping one system as the source of truth (either Shopify or one inventory management app) and making sure everything else only reads from it, not edits stock on its own. I also turn off stock updates in apps like bundles, preorders, or shipping tools so they don’t create mismatches.
A few simple habits that really help:
-
Use Shopify Locations properly and always log transfers and returns
-
Do stock counts regularly and pause sales during counts if you can
-
Avoid letting inventory go negative
-
Check audit logs when numbers look off
Once everything flows from one place and fewer tools touch inventory, the “available vs on-hand” problem gets much easier to manage.
May this will help you…
Hey @eric18,
It sounds like you’ve done great work in keeping your inventory accurate! Especially not making manual changes in Shopify Admin and not regularly counting, these are easy options that can lead to inventory nightmares.
If you need any help with stock taking and counting, to speed up your manual counts https://apps.shopify.com/stock-take-inventory-count-1
It integrates into Shopify POS, if you are using that for your store. So no need to learn any new systems.
It supports barcode scanning if you have other physical products, but you can also manually count..
If I can help you with this at all, please let me know,
Jordan
Hey Eric18, we do warehouse management and our company started using tmaiot.com. We track stock with RFID readers, it’s much easier than counting everything by hand 