MSP billing software turns contracts, prepaid hours, time, and expenses into invoices, then hands them to your accounting. For an MSP with 1 to 15 technicians, our pick is SherpaDesk: contracts with prepaid hours and overage, invoices built from ticket time, and QuickBooks Online sync.
Key takeaways
A helpdesk and PSA (professional services automation) a small IT team can run alone. No contract. No implementation project. No dedicated admin.
| If you… | Pick | Price | Catch |
|---|---|---|---|
| Bill contracts, prepaid hours, and overage from the helpdesk | SherpaDesk | Base Camp from $45 per agent per month ($40 billed annually); first agent free | We don't build RMM. We integrate with yours, and the stack stays yours. |
| Want invoices, time, and expenses in QuickBooks Online | SherpaDesk | Base Camp from $45 per agent per month ($40 billed annually) | Time sync needs QuickBooks Online Essentials or Plus |
| Sell per-user bundles and want prepaid hours that roll forward | DeskDay | $79 per tech per month ($59 a month billed annually) | 2-seat minimum on monthly billing |
| Want card autopay and Pax8 license data in billing | Syncro | Core $159 per user per month ($129 on the annual plan, paid monthly) | Accounting sync is mostly one way |
| Resell Microsoft CSP licenses | HaloPSA | $99 per agent per month, billed annually (monthly equivalent) | Onboarding package required |
Prices as of October 2026.
For a team of 3, SherpaDesk Base Camp starts at $90 a month, or $80 a month billed annually, because the first agent is free. DeskDay Standard is $237 a month ($177 a month billed annually), and Syncro Core $477 a month ($387 a month on the annual plan, paid monthly). HaloPSA is a $297 monthly equivalent, billed annually, plus required onboarding.
Picks By Scenario Comparison Table Cost For A Small Team Billing Day Calculator How To Choose FAQHow we chose
We publish this guide and include our own product among the 8 tools, with the same template and its limitations.
For the wider stack, see our guide to the best MSP software.
| Tool | Entry price | Prepaid hours and overage | Accounting handoff | Trial |
|---|---|---|---|---|
| SherpaDesk Ours | Base Camp from $45 per agent per month ($40 billed annually); first agent free | Included hours, overage, alerts, new prepaid pack | QuickBooks Online sync; Xero; FreshBooks; QuickBooks Desktop by .IIF file export | 14 days free, no card |
| DeskDay | $79 per tech per month (2-seat minimum), $59 a month billed annually | Prepaid and block hours; overage, pause, auto-renew, or roll forward | QuickBooks Online, Xero | 14 days |
| Syncro | Core $159 per user per month; $129 on the annual plan, paid monthly | Prepay hours; extra hours at the standard or contract rate | QuickBooks Online, Desktop (Windows connector), Xero; one way, except optional payment sync from QuickBooks Online or Xero and a one-time QuickBooks Online customer import at setup | 14 days, no card |
| HaloPSA | $99 per agent per month, billed annually, plus onboarding | PrePay with thresholds and auto top-ups | QuickBooks two-way; Xero payments sync back | 30 days, no card |
| Autotask (Kaseya 365 Ops) | $129 per user per month, 3-user minimum, one-year term | Block Hours and Retainer contracts | QuickBooks Online and Desktop; Xero via a third-party connector | Not stated |
| ConnectWise PSA | Quote; billing on Pro | Recurring blocks that roll over or expire | Batch posting; payments sync from accounting only | Not stated |
| Gradient Reconcile | $299 a month, up to 150 customers with active contracts | Add-on: license counts | Through your PSA | Not stated |
| FlexPoint | Starter $249 a month, plus card and ACH fees | Add-on: payments | QuickBooks Online, Desktop, Xero | Not stated |
Prices as of October 2026.
For a team of 3, SherpaDesk Base Camp starts at $90 a month ($80 a month billed annually). DeskDay is $237 a month ($177 a month billed annually), and Syncro Core $477 a month ($387 a month on the annual plan, paid monthly).
Kaseya 365 Ops is $387 a month on a one-year term, and HaloPSA a $297 monthly equivalent plus onboarding. Gradient ($299 a month) and FlexPoint ($249 a month plus fees) are add-ons you pay on top of a PSA.
Best for MSPs of 1 to 15 technicians that bill contracts, prepaid hours, and overage from the helpdesk
$45 per agent per month on Base Camp ($40 billed annually) · High Camp $55 per agent per month ($50 billed annually)
Each client gets its own rate plan: hourly, fixed plus hourly, retainer, blended hourly, or contract-level. A Flat + Hourly contract carries included hours, bills overage at contract rates, and adds weekly or monthly recurring expenses. Two founders who ran their own MSP have built it since 2001.
Recommendation
Choose SherpaDesk if the people who work the tickets also send the invoices, and you want prepaid hours tracked in the contract, not a spreadsheet.
Consider another option if most of your invoice is resold licenses that change every month.
Best for MSPs that sell per-user bundles and want prepaid hours that roll forward
$79 per tech per month, billed monthly · $59 a month billed annually · Enterprise $1,189 a month for 10 seats, annual commitment
You can mix hourly, block-hour, flat-fee, and per-seat plans, even for one client. A seat-based contract bundles tools and remote labor into one per-user price. Unused prepaid hours can roll forward.
Recommendation
Choose DeskDay if you sell per-user bundles with block rules per client.
Consider another option if you need a documented QuickBooks Desktop connection; it isn't listed.
Best for MSPs that want card autopay on recurring invoices and Pax8 license data in billing
$159 per user per month on Core · $129 on the annual plan, paid monthly · Team $209 per user per month ($179 on the annual plan, paid monthly)
With a payment gateway and a saved card, a recurring invoice charges the client automatically. Labor past a prepaid block bills at the standard or contract rate. Pax8 "procurement and license data" flows into billing.
Recommendation
Choose Syncro if card autopay and Pax8 data matter more to you than the license cost.
Consider another option if your bookkeeper edits invoices or customers in accounting and expects those edits in the PSA.
Best for MSPs that resell distributor and Microsoft CSP licenses and can fund onboarding
$99 per agent per month, billed annually (USD, named license, 1 to 24 agents) · one plan, no tiers
PrePay contracts get balance thresholds and auto top-ups. Halo connects to your distributor and Microsoft CSP "to automate fluctuations in counts," and payments added in Xero sync back.
Recommendation
Choose HaloPSA if resold licenses drive your invoices and you have budget for an onboarding project.
Consider another option if you want to start this week without one.
Best for MSPs that want PSA, documentation, and quoting in one subscription
$129 per user per month in Kaseya 365 Ops · one-year term · Autotask alone: quote
Kaseya 365 Ops bundles Autotask with IT Glue, Kaseya Quote Manager, and ConnectBooster. Autotask has six contract types, including Block Hours and Retainer, and sends invoices to QuickBooks Online every 15 minutes. Autotask reaches Xero through ApplicationLink, a third-party connector that transfers invoices as sales orders for a flat monthly fee (amount not published).
Recommendation
Choose Autotask if you'd buy IT Glue anyway and can commit to a year.
Consider another option if you need fewer than 3 Kaseya 365 Ops licenses.
Best for MSPs that post prepaid agreements to deferred revenue and have someone to run the setup
Quote only · billing, agreements, and accounting sync on the Pro package
A Recurring Block agreement sells "a recurring block of dollars or hours" each month, and the hours can roll over or expire. A prepayment agreement posts the first charge "to a deferred revenue account," and "Allow overruns" lets a client use hours from a future month.
Recommendation
Choose ConnectWise PSA if your accountant wants prepaid blocks posted to deferred revenue from the PSA.
Consider another option if you want a price before a sales call.
These sit on top of a PSA for one MSP billing job: license counts or collections. One r/msp member said manual checks "always found a couple grand we were missing".
Best for MSPs whose invoices are mostly resold licenses, on Autotask, ConnectWise, HaloPSA, or Syncro
$299 a month for up to 150 customers with active contracts · Grow $699 a month · Scale $999 a month
Reconcile finds "mismatched counts across PSA, vendor, and distributor systems." It connects to distributors such as Pax8 and Sherweb, and to six PSAs.
Recommendation
Choose Gradient Reconcile if license counts drift every month and you already run a PSA it lists.
Consider another option if most of your invoice is labor and flat fees.
Best for MSPs on Autotask, ConnectWise, HaloPSA, or SuperOps that want autopay and past-due reminders
$249 a month on Starter · Growth $550 a month · Plus by quote
FlexPoint handles AutoPay, past-due reminders, and deposit reconciliation. It integrates with QuickBooks Online, QuickBooks Desktop, and Xero.
Recommendation
Choose FlexPoint if invoices go out on time but the money comes in late.
Consider another option if your PSA isn't on its integration list.
SuperOps prices per endpoint, by quote, with a 150-endpoint minimum. RackNap's Standard plan, labeled for MSPs and ISVs, is $10K a month plus setup and transaction fees.
QuickBooks Online Essentials is $85 a month for 3 users (30-day free trial or 50% off for 3 months). Xero Growing is $59 a month at its regular price. For 3 technicians, SherpaDesk Base Camp starts at $90 a month ($80 a month billed annually).
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| Tool and plan | Month to month | Annual plan, per month | What else you pay or accept |
|---|---|---|---|
| SherpaDesk Base Camp Ours | $90 | $80 a month, billed annually | First agent free, so 3 agents pay for 2; no onboarding fee |
| DeskDay Standard | $237 | $177 a month, billed annually | 2-seat minimum and optional $800 onboarding, monthly plans |
| Syncro Core | $477 | $387 a month on the annual plan, paid monthly | Microsoft 365 license billing on Team: $627/month, or $537/month on the annual plan |
| HaloPSA | Price not published | $297 monthly equivalent, billed annually | Required onboarding package |
| Autotask in Kaseya 365 Ops | $387 a month on a one-year term | 3-user minimum; card and ACH fees extra | |
| ConnectWise PSA | Quote | Billing on Pro; implementation sold separately | |
| Gradient Reconcile Launch | $299 a month (billing period not stated) | On top of your PSA; Microsoft add-on $199 a month | |
| FlexPoint Starter | $249 a month plus fees (billing period not stated) | On top of your PSA; card 3.0%, ACH $1 per transaction | |
Prices as of October 2026.
For a team of 3, SherpaDesk Base Camp starts at $90 a month month to month, or $80 a month billed annually.
Definition
MSP billing turns contracts, prepaid hours, time, and expenses into invoices, then passes them to accounting and collects payment.
TechTarget describes PSA software as one system that replaces "separate tools for resource planning, billing, time tracking and project management". Capturing the hours is covered in billable hours tracking, and which contract to sell in managed services pricing.
The owner of a four-person MSP with about 30 clients put month-end invoicing at "Anywhere from 8 to 12 full hours." The same owner wrote, "at month end I tally up the hours for each client and then deduct from the block hour total". A two-person MSP found cloud backups running "since 2023" that it "never billed".
In Atradius's 2026 North America survey, delayed payments hit seven in ten firms on average, and 23% of B2B receivables.
Hours a month spent building invoices
invoices × minutes ÷ 60, rounded up. Your numbers stay in the browser.
Test these five things with last month's invoices.
Sort last month's invoice lines by type, then answer two questions.
Then run one real month in each finalist.
One r/msp member said block hours "tend to linger and complicate billing". Put the expiry rule in your managed services agreement, and ask your accountant how to book unused hours.
How this works in SherpaDesk
A helpdesk and PSA a small IT team can run alone. You set up a contract with prepaid hours, rate plans, and recurring expenses. Ticket time counts against the included hours, then bills as overage. An alert fires as the contract nears or passes its included hours. From the account's Contracts tab, you move the overage into a new prepaid pack.
"Ready to Invoice" lists uninvoiced time and expenses by contract, and bulk "Create & Send" sends the invoices. Invoices then sync to QuickBooks Online.
Pricing is per agent, and your first agent is free, forever. Base Camp starts at $45 per agent per month ($40 billed annually).
Where SherpaDesk fits
You get contracts, prepaid hours, and invoices from the helpdesk. If resold licenses from a distributor make up most of each invoice, HaloPSA or a reconciliation tool fits that job better; Gradient doesn't list SherpaDesk among its PSAs.
For an MSP of 1 to 15 technicians billing labor and prepaid hours, our pick is SherpaDesk. Contracts carry included hours and overage, and invoices sync to QuickBooks Online. Base Camp starts at $45 per agent per month, and the first agent is free, so a team of 3 pays $90 a month.
MSP means managed service provider. TechTarget defines it as "a third-party company that remotely manages a customer's information technology (IT) infrastructure and end-user systems". "MSP software" usually means the tools that business runs on: a PSA for tickets, contracts, and invoices, and remote monitoring and management (RMM) for client devices.
In medical billing, MSP means Medicare Secondary Payer. CMS says the program exists "to ensure that Medicare is aware of situations where it should not be the primary, or first, payer of claims". Here, MSP billing means billing by managed service providers.
There are three setups: billing inside a PSA such as SherpaDesk, Syncro, or HaloPSA; a PSA plus an add-on such as Gradient or FlexPoint; or accounting software on its own. Labor and prepaid hours point to a PSA; mostly resold licenses point to an add-on. See the Comparison Table.
By revenue, CRN's 2026 Solution Provider 500 ranks Accenture No. 1 for the sixth year in a row, followed by Tata Consultancy Services and NTT Data. The list covers VARs, systems integrators, and IT consultants with operations in North America, not only MSPs.
The client pays up front for a block of hours. Each time entry draws the block down, and work past zero bills as overage or starts a new block. In your books, a prepayment is a contract liability until the hours are used or expire. How to recognize unused hours is a question for your accountant.
Patrick co-founded SherpaDesk and has led it as CEO since 2013. He has worked with IT service providers since 1998, first on network projects for schools and government offices, then on the helpdesk software their technicians use every day.