QuickBooks Desktop to Stratus QuickBooks Online Migration

What this is

This guide covers moving a company in Contractors Cloud from the QuickBooks Desktop integration (which syncs through Intuit's Web Connector) to the QuickBooks Online integration (which syncs through a direct, real-time connection). It runs alongside Intuit's own conversion of your Desktop company file into a QuickBooks Online company — most of the migration happens on the QuickBooks side; this article covers the Contractors Cloud side and how to sequence the two so nothing double-syncs.

Why move to QuickBooks Online

It keeps working. Intuit is phasing out QuickBooks Desktop, so most Desktop customers will need to move to QuickBooks Online.
Real-time, two-way sync. Desktop can only export to QuickBooks on a 10-minute Web Connector poll. Online supports 2-way sync and updates immediately — paid status and QuickBooks-side edits can flow back into Contractors Cloud automatically.
No local app to babysit. There's no Web Connector to keep running on a specific PC; the connection lives in the cloud.

The migration has two halves

Side	What happens	Who does it
QuickBooks (Intuit)	Your Desktop company file is converted into a new QuickBooks Online company. Every QuickBooks record is re-created and given a new QuickBooks ID.	You + Intuit (see the links at the bottom)
Contractors Cloud	Disconnect the Desktop integration, switch the company to Online, reconnect, and re-import your lists so Contractors Cloud re-links to the new Online records.	You / your Contractors Cloud admin

⚠️ Sequence matters. Disconnect QuickBooks Desktop in Contractors Cloud before you rely on the new Online connection. Running both at once can push duplicate transactions into QuickBooks.

Quick start (minimum steps)

Disconnect QuickBooks Desktop completely (Web Connector + Contractors Cloud) — see below.
In QuickBooks, convert your Desktop company file to QuickBooks Online (Intuit's tool).
In Contractors Cloud, Company Settings → QuickBooks → QuickBooks Type, change QuickBooks Desktop to QuickBooks Online.
Connect your QuickBooks Online account (see the QuickBooks Online article for the connection steps).
Set your QuickBooks Sync Start Date so old history isn't re-pushed into the new company.
Re-import your lists from QuickBooks Online: Accounts, Items, Terms, Tax Codes, Classes, Vendors.
Choose your sync modes, then verify a few records before turning on automatic sync.

Step 1 — Disconnect QuickBooks Desktop completely (do this first)

Why this is required. The Web Connector keeps polling Contractors Cloud every ~10 minutes and pushing queued transactions into whatever Desktop file it's pointed at. If it keeps running after you've moved to Online, it will push into the old, now-frozen Desktop file — and if two connectors ever point at one company file, you get duplicate transactions. QuickBooks Online also assigns brand-new IDs to every record, so a half-connected Desktop integration leaves Contractors Cloud holding stale links.

Disconnecting means all of the following:

Remove Contractors Cloud from the QuickBooks Web Connector. On the PC that hosts the Desktop company file, open the QuickBooks Web Connector, select the Contractors Cloud application, and Remove it (then close the Web Connector). This stops all Desktop polling. Contractors Cloud can't do this for you — it lives on your machine.
If you ran QuickBooks Desktop through Classic Contractors Cloud, disconnect it there too. You can only have one Web Connector pointed at one company file. If an old Classic connection is still registered, remove that connector app as well — see Stratus vs. Classic gotchas below.
Switch the company to Online in Contractors Cloud. Go to Company Settings → QuickBooks, and change QuickBooks Type from QuickBooks Desktop to QuickBooks Online. Contractors Cloud immediately stops queuing Desktop work for this company and drops its Web Connector profile link.

Note: A single Web Connector profile can be shared by more than one company. Switching one company to Online doesn't delete a shared profile that other companies still use — that's expected. It only unlinks this company.

Step 2 — Convert your company file in QuickBooks (Intuit's side)

This part is done in QuickBooks, not Contractors Cloud. In QuickBooks Desktop (Pro/Premier 2022 or later): Company → Export Your Company File to QuickBooks Online, then follow the on-screen checklist. Intuit uploads and converts the file and emails you when your company "is now Online." Use Intuit's official guides (linked at the bottom) — they own this step, including what does and doesn't convert 1:1.

Step 3 — Connect QuickBooks Online in Contractors Cloud

With QuickBooks Type now set to QuickBooks Online, connect the new company:

Confirm QuickBooks Online is enabled for the company (your Account Manager can turn it on if needed).
Connect your QuickBooks user, then connect the company's QuickBooks Online company (realm). Detailed connection steps are in the QuickBooks Online article.
Set the QuickBooks Sync Start Date. This limits which documents are eligible to sync so you don't re-push years of already-converted history into the fresh Online company.
Set your sync modes — INVOICE SYNC, CREDIT MEMO SYNC, PAYMENT SYNC, VENDORS & BILL SYNC. On Online you'll now see a 2-way sync option that Desktop never had.

Step 4 — Re-import your lists from QuickBooks Online (required)

This step is not optional. The conversion gave every QuickBooks record a new ID, so the links Contractors Cloud stored during the Desktop era no longer point anywhere. Contractors Cloud re-establishes reference links by a fresh import from QuickBooks Online — not by reusing your old Desktop links.

In Company Settings → QuickBooks, run each of these (they read from the newly connected Online company):

Import Accounts from QuickBooks
Import Items from QuickBooks
Import Terms from QuickBooks
Import Tax Codes from QuickBooks
Import Classes from QuickBooks
Import Vendors from QuickBooks

Contractors Cloud never exports your chart of accounts — accounts are import-only, by design. Importing here simply re-links your existing Contractors Cloud accounts to the matching Online accounts.

Step 5 — Historical transactions & avoiding duplicates

Your new Online company already contains everything Intuit just converted (invoices, bills, payments, etc.). To avoid Contractors Cloud re-creating those as duplicates:

Lean on the QuickBooks Sync Start Date. Set it so only go-forward documents are eligible to sync. Everything dated before it is skipped.
Verify before you automate. Open a few migrated invoices, payments, and bills and confirm they map to the right Online records before enabling automatic sync.
Historical re-linking is a hands-on step. Reference lists re-link themselves via the imports above, but individual historical invoices/bills/payments do not have a self-serve "re-link to the converted Online record" button. If you need history reconnected rather than simply left in QuickBooks, contact your Account Manager / ThinkUp support to coordinate it.

Stratus vs. Classic QuickBooks Desktop — gotchas

If your company previously ran QuickBooks Desktop through Classic Contractors Cloud, keep these differences in mind:

One connector per company file — always. The Web Connector .qwc file points at a specific system (Classic or Stratus). Two connectors polling the same company file will double-post. During any move, remove the old connector app before (or as) you register the new one.
Web Connector Profiles live under Company Settings → QuickBooks in Stratus. That's where you download the .qwc file and see the connector password. A profile can be shared across companies, which is why switching one company to Online doesn't remove a shared profile.
Desktop is export-only; Online adds 2-way sync. The sync-mode options differ — Desktop has no 2-way sync choice. Don't expect the two integrations to behave identically after the move.
Don't reconnect Desktop "just in case." Once you're on Online, leaving any Desktop connection alive is the single most common cause of duplicate records.

Troubleshooting

Symptom	Cause	Fix
Duplicate transactions appear in QuickBooks after migrating	A Web Connector is still running, or two connectors point at one file	Remove every Desktop Web Connector for this company (Step 1); rely only on the Online connection
Records show as unmapped / won't link in QuickBooks Online	Reference lists weren't re-imported after the conversion	Run the Import … from QuickBooks buttons (Step 4)
"QuickBooks blocked this because it falls in a closed accounting period"	The document is dated inside a closed period; QuickBooks Online won't let an app post there	Enter it directly in QuickBooks, or ask your bookkeeper to move the closing date (see the QuickBooks Online article)
Old Desktop data is still trying to sync	The company wasn't switched to QuickBooks Online in Contractors Cloud	Set Company Settings → QuickBooks → QuickBooks Type to QuickBooks Online