3PL: How to Reconcile 3PL Carrier Bills – ShipHero

In high-volume warehouse management, accurate billing is as critical as shipping speed. ShipHero’s Carrier Reconciliation tool bridges the gap between quoted carrier rates and the actual billed charges.

Accurate data ensures your warehouse remains profitable. ShipHero uses reconciliation data to balance shipping costs against customer billing. Because the system is designed for financial transparency, errors like duplicate imports or incorrect file formatting can create significant administrative hurdles if not caught early.

How Carrier Reconciliation Works

ShipHero links uploaded carrier invoice data to shipments using the tracking number.

The system compares the quoted cost (at time of shipping) to the actual cost (from the carrier).
If a difference is found, a list of "label reconciliations" appear on the customer's billing page.
Adjustments are automatically added to the customer's next bill.

IMPORTANT NOTE: Carrier reconciliation files cannot be deleted once uploaded. Always double-check your data before performing a bulk upload.

IMPORTANT NOTES:

The carrier selected is used to filter shipping labels. The system searches for shipping labels that match both the tracking number AND the carrier. This prevents false matches when the same tracking number format might exist across different carriers.

Exception: When Endicia is selected as the carrier for the reconciliation CSV upload, ShipHero searches both "endicia" and "usps" carriers since Endicia uses USPS for delivery.

So if you select "Canada Post" from the dropdown, the reconciliation will only match tracking numbers from labels that were created with Canada Post as the carrier - not UPS, FedEx, or any other carrier, even if a tracking number somehow matched.
ShipHero uses the label cost charged by the carrier. If a carrier lists duties, taxes, and surcharges separately (for example, in a column called "Taxes"), ShipHero might not detect them when reconciling the bill.
Duplicate tracking number consolidation process: To prevent overcharging, ShipHero handles duplicate tracking numbers differently based on how you upload the reconciliation CSV:

Scenario	Logic	Result
Single File Upload	ShipHero uses a deduplication process to combine multiple charges for a single tracking number when submitted in a single CSV.	One unique record per tracking number.
Multiple File Uploads (Separate jobs)	The system treats every upload as a unique Job ID and does not check for duplicate tracking numbers across jobs.	Duplicate charges for the same shipment.

Best Practices for Success

The "Test Row" Strategy: Before a bulk upload, create a CSV with only the first 2 rows. Upload it to ensure columns (weight, zone, tracking number) map correctly.
Consolidate Files: Combine all carrier data into a single master CSV before uploading. This triggers ShipHero’s internal deduplication to merge multi-line charges.
Centralized Management: Assign one team member to handle uploads to prevent redundant data entry.
Audit Surcharges: Remember that ShipHero sums the base rate and surcharges. If a cost looks high, it is likely the total of all fees for that tracking number.

How to Reconcile Carrier Invoices

Go to the 3PL Billing > Reconcile page and click the Reconcile Carrier Bill button (top left).
Select your Carrier from the dropdown.
- For FedEx, UPS, and Endicia reconciliations you have the option to directly upload the carrier's CSV invoice or upload your own CSV using the "Other" option. Instructions on how to export your invoices CSV files for FedEx, UPS, and Endicia are provided below.
- For all other carriers, please select the "Other" option and then select the carrier from the dropdown in the next module. When "Other" is selected you will need to upload a CSV using the reconciliation CSV template and guidelines provided below.
Upload your CSV. Specific instructions on how to export your carrier invoices and format a custom reconciliation CSV can be found below.

How to Export Your FedEx Invoice CSV File

Go to https://www.fedex.com/billing-online
Under “Billing Center Quick Links” click on “Invoices”.
Click on the invoice number to access the invoice summary.
On the “Invoice Summary” page click on the “View/ Download Invoice Data” button.
From the modal select the “FedEx Billing Data (.csv format, 250 data elements)” option and click on the Submit.

How to Export Your UPS Invoice CSV File

Go to http://www.ups.com/billingcenter
Under “Billing Center Quick Links” click on “Invoices”.
Click on the invoice number to access the invoice summary.
On the “Invoice Summary” page click on the “View/ Download Invoice Data” button.
From the modal select the “UPS Billing Data (.csv format, 250 data elements)” option and click on the Submit.

How to Export Your Endicia Invoice CSV File

Follow the steps described in this article from the Endicia Online Account Help.
Be sure to have the report include all charges applicable to specific shipping labels identified by their tracking numbers by selecting them in the Show field.
Check the Export check box in order to have the report exported as a CSV file.

Uploading a Reconciliation CSV when "Other" is Selected

You can reconcile tracking numbers from any carrier by using the Reconciliation CSV template. Please pay attention to the required fields and follow the steps below:

Download the CSV (comma separated values) file template. You can open it with any spreadsheet app.
There are three groups of columns you can populate, only the first of which is mandatory.
- Fields for charge reconciliation (required): This is the basic data from the carrier bill with which we'll reconcile differences between the estimated shipping cost at label printing time and the amount billed by your carrier for that tracking number.
  - Date
  - Tracking number
  - Billed amount
- Breakdown of billed amount (optional): This is the general breakdown of the amount billed by your carrier for each tracking number. Depending on your carrier, some of these details may not be present in your carrier bill, and that's OK. These fields are not required for the reconciliation, they'll be used to provide insight into your business.
  - Taxes
  - Freight charges
  - Misc charges
  - Discount
- Additional Fields (optional): You may extend the file with any number of additional columns. They will be stored alongside the reconciled data and displayed for reference purposes.
Edit your data into it and upload. Keep in mind that if you are on a Mac, you'll need to set the format to "Windows Comma Separated."

Troubleshooting Errors

If you upload incorrect data, use these three paths to resolve it:

Manual Exclusion: Before finalizing a client's bill, review pending charges and manually exclude incorrect records.
Status Monitoring: Check the job status (NEW, PENDING, COMPLETED, ERROR). Records in ERROR status will generally not proceed to billing.
Engineering Support: If a record must be deleted from the database entirely, you must contact ShipHero Support.

Additional Resources:

How to Set Up Carrier Billing for 3PL Clients