The Shopify Fulfillment Network Reconciliation Service That Finds Your Missing Units and Files What Your Records Prove.
The Fulfillment Network app in your Shopify admin connects you to Flexport, which has run the network since it bought Shopify’s logistics business in 2023. Flexport receives, stores and ships your units, and when the counts drift, the claim goes to Flexport on Flexport’s clock. We take these case by case and scope each one at a free assessment, unit by unit.
This window is what your storefront can sell. Each carton is ten units at Flexport. Change the scene and watch the shelf and the numbers disagree.






Six Ways Your Shopify Fulfillment Stock Goes Missing
Most merchants hear about each of these from a notification they swiped away. Swipe through the six and see what each one leaves behind.
Shipment 58213: 460 of 480 units received.
6 units of TEE-BLK-M. Cause determination available.
No tracking update since the label was scanned.
I ordered black, the package had navy.
Order #1033 return delivered to the warehouse.
12 units of MUG-WHT-12 moved to Under Investigation.
These are the six messages that mean stock went missing or unpaid. Swipe the top one away, or tap clear, to see what the next one is really saying.
Each Shopify Fulfillment Claim Has Its Own Clock
A receiving discrepancy needs the shipment or ASN ID, the expected and received counts, and a commercial invoice or wholesale cost record, raised within 90 days of arrival. An order claim is due within 30 calendar days of the promised delivery date. Damage found in the warehouse gives you 7 calendar days before the units are disposed of.
Flexport values a claim from your cost. It pays approved order claims at wholesale value plus the fulfillment fees charged, and falls back to a share of retail only when there’s no invoice. So the invoice is the first thing we ask you for.
- Shipment or ASN ID on every inbound claim
- Commercial invoice before any figure
- Packaging checked first, since damage from weak packaging stays with the seller
Pick a claim type, then roll evidence into the cart. Flexport reads each claim type against its own list, and extra items do not make a claim stronger.
How We Work Your Claim From Report to Invoice Credit
Five steps, in order. Each one is finished and filed before the next one starts.
Every step is a slip, and each one goes on the spike only when it is finished. Tap Slip 01 to start.
One App in Shopify, Another Set of Names at Flexport
Shopify sold its logistics business, Deliverr included, to Flexport in 2023. The Fulfillment Network app still sits in your Shopify admin, but receiving, storage, shipping and claims run on Flexport’s side, under Flexport’s names. Knowing both sets of names is half the work. Slide the jaw and read both scales.
Stage 01 of 06
One unit, two naming systems. Drag the sliding jaw along the beam and read both scales at the hairline.
Every Flexport Credit Matched Back to Its Claim
Flexport pays approved claims as credits on your billing invoice, with no separate deposit. We match each credit to the claim that earned it, so you can see what was filed, what was paid and what’s still open.
- Receivingnot counted
- Damagenot counted
- Lost ordersnot counted
- Wrong itemnot counted
- Returnsnot counted
- Feesnot counted
Credits from Flexport land on your invoice, so they are easy to lose track of. The drawer is open. Tap a compartment and count it against what was filed.
Shopify Fulfillment Network Reconciliation FAQs
Don’t see your question? Send us your Fulfillment Network records and we’ll answer it directly.
Who runs the Shopify Fulfillment Network now?
Flexport runs the warehouses, receiving and claims behind Shopify’s fulfillment app. Shopify sold its logistics business to Flexport in May 2023 in exchange for a stake in Flexport. Merchants still connect through the app in the Shopify admin, but inventory problems and claims are handled under Flexport’s policies.
What do I do if Flexport received fewer units than I sent?
If Flexport received fewer units than you sent, open a claim for the inbound shipment with Flexport support. Include the shipment or ASN ID, the unit count affected, a description of any damage and a commercial invoice or cost documentation. Compare your packing list to the received count first so every missing unit is accounted for.
How long do I have to file a Flexport inbound claim?
Flexport gives merchants 90 days from the shipment’s arrival or the incident date to file a claim for an inbound shipment that is lost, damaged or missing units. Claims submitted after 90 days are not processed. Check receiving counts as soon as each shipment arrives so gaps are raised well inside that window.
How long do I have to file a Flexport removal claim?
Flexport gives sellers 7 calendar days from the final delivery date to file a removal order claim, extended to 30 calendar days during peak season from November 15 to January 15. That is a short window, so open and count every removal shipment the day it arrives and photograph any damage before you unpack.
What documents does Flexport need for a claim?
Flexport claims need the shipment or ASN ID, the number of units affected, a description of the damage and a commercial invoice or other cost documentation that proves the value. Photos of cartons and labels help on damage claims. Never create or edit an invoice to support a claim, since one bad document can sink the rest.
Does Flexport pay for damage caused by poor packaging?
Damage that traces back to weak or improper packaging generally stays with the merchant, so a claim will not fix it. Check that your cartons, inner packing and labels meet Flexport’s inbound requirements before the next shipment. Fixing the packaging stops the same damage from coming back every month.
Is the Shopify fulfillment app a Shopify service or a Flexport service?
It is both in practice. You connect through the fulfillment app in your Shopify admin, but since Shopify sold its logistics business to Flexport in 2023, Flexport runs the warehouses, the receiving and the claims. That is why claim windows and payout rules come from Flexport’s help center.
Can Flexport claim windows change?
Yes. Flexport publishes its claim windows and payout rules in its help center and can update them. Check the current policy before you file anything, and keep a record of the version you relied on. Working the oldest gaps first protects you if a window is shorter than you expected.
Is it worth hiring a Shopify fulfillment reconciliation service?
A fulfillment reconciliation service is worth it when you send enough inventory through Flexport that nobody matches every receiving count, order and removal to your records. We match units across Shopify and Flexport, file each gap once inside its window and flag packaging problems. Start with a free assessment of your fulfillment records.
How much does Shopify fulfillment reconciliation cost?
The cost of fulfillment reconciliation depends on your shipment volume, SKU count and how many gaps are still inside Flexport’s windows. We start with a free assessment, show you what looks claimable and then quote the work. The price follows how much there is to reconcile and how hard the gaps are to prove.
Can anyone guarantee Flexport will pay my claim?
No. Flexport makes the final decision on every claim and the amount credited. Be careful with anyone who promises a payout. What we commit to is the work: every documented gap filed once, inside its window, with the right proof, and a straight answer on what is worth filing before you pay.
Services That Pair With Shopify Fulfillment Reconciliation
Hover a service to see what it adds to this one.
Amazon inventory reconciliation
If you also sell through FBA, it’s the network we reconcile most, with its own reports and windows.
- Inbound and in-storage losses
- Refunds with no return
- A monthly reconciliation log
Merchant processor disputes
Your Shopify store carries chargebacks too. Disputes run on a different clock from fulfillment claims.
- Chargebacks answered with evidence
- Reason codes read first
- Processor reserves reviewed
Consultation
Not sure the gaps are worth filing? The consultation is an honest look before any work starts.
- Records reviewed first
- A straight answer on viability
- No filing without a case
Get a Free Assessment of Your Shopify Fulfillment Records
Send us a month of Fulfillment Network orders and Flexport inventory records. We’ll tell you if there’s a case worth filing before you pay anything.