MSP Billing and Reconciliation

Making ConnectWise and QuickBooks Work Together

If you’ve ever tried syncing ConnectWise Manage with QuickBooks Online (QBO), you know that MSP billing and reconciliation can get messy fast.

At our MSP, we used Mobius and ConnectBooster as middleware to pull invoices from ConnectWise Manage into QBO. This handled the basics — invoices synced reliably and clients could pay through the portal — but the real challenge was behind the scenes: accurate MSP financial reconciliation.

TL;DR:

• Use Mobius + ConnectBooster for invoice sync between ConnectWise and QBO.
• Work with Visionary360 to set up proper GL mappings.
• Implement ConnectWise Procurement for accurate COGS and revenue timing.
• Use Junto to automate MSP billing reconciliation and eliminate missed revenue.

Getting MSP GL Mapping Right

Aligning general ledger (GL) mappings between ConnectWise and QBO is a critical step in MSP billing accuracy. Every revenue stream and cost needs to map correctly for your books to balance.

If this process feels overwhelming, Visionary 360 is a great partner. They specialize in ConnectWise Business Management and can help MSPs clean up GL structures before automating.
We ran the CW Business Management SKU, and their expertise was invaluable.

Fixing MSP Revenue Timing with ConnectWise Procurement

In 2025, we implemented the Procurement Module within ConnectWise, including purchase orders (POs).

This finally fixed one of our biggest issues: COGS (cost of goods sold) and revenue timing.
Before that, our monthly financial reports were always off. After the change, our MSP billing cycles matched our actual costs and revenue in QBO, giving us clean, real-time visibility.

The MSP Billing Challenge: Vendor Reconciliation

Even after cleaning up our accounting, one major issue remained — vendor invoice reconciliation.

Vendors like Pax8 and TD Synnex often send large lump-sum invoices. Without detailed mapping, it’s nearly impossible to align software revenue and COGS by client.
This makes MSP billing reconciliation incredibly difficult and often leads to missed revenue opportunities.

How Junto Automates MSP Billing Reconciliation

This exact problem inspired one of the core features we built at Junto.

Junto automatically reconciles your Pax8 or TD Synnex invoices with Microsoft and ConnectWise license counts. This ensures your MSP billing system stays aligned with your vendor costs and customer invoicing — automatically detecting mismatches before they impact your margins.

No more manual spreadsheets.
No more missed billing.
Just accurate, automated reconciliation.

Why MSP Billing Optimization Matters

At Junto, we focus on finding the hundreds of small wins that help MSPs get their margins back.

From better ConnectWise–QuickBooks synchronization to automated MSP billing reconciliation, every percentage point of improvement adds up to stronger profitability and happier clients.