How it runs for SaaS companies and venture-backed startups
Our cash application desk applies every receipt in QuickBooks Online or Xero within a business day using remittance advices, AP portal data and the billing system, logs short payments with reasons and clears unapplied cash before each close so the aged receivables report is accurate.
What is cash application?
Cash application means matching money received from customers to the invoices it pays and recording that in the accounting system. It covers bank receipts, checks, lockbox files, card payouts and remittance advices, including partial payments, deductions and payments with no reference. Done well, the aging is accurate and no customer is chased for an invoice they already paid.
What we handle for SaaS companies and venture-backed startups
- Apply ACH and wire receipts from enterprise customers to invoices within 1 business day
- Split payments that settle several invoices using remittance and portal data
- Log short payments against disputed usage lines or bank fees with the reason
- Sync applied payments back to Stripe Billing or Chargebee so invoice status matches
- Clear unapplied cash to zero at every month-end close
The KPI that matters here
95% of enterprise receipts applied within 1 business day with invoice status in the billing system matching the ledger.
SaaS compliance notes
ASC 606 and IFRS 15 revenue recognition
Revenue is recognized when performance obligations are satisfied: subscriptions ratably over the term, usage as consumed, implementation fees over the period your accountant determines, and multi-element contracts allocated on standalone selling prices. We apply the policy your CPA or auditor sets and document the judgment for each contract type. Investors and acquirers expect this from the first institutional round.
Deferred revenue and contract liabilities
Cash collected ahead of service is a contract liability, not income, and the balance must roll forward every month: opening, billings, revenue recognized, closing. We maintain that schedule by customer and contract and tie it to the balance sheet and to the billing system, which is the first thing a diligence team tests.
Sales tax, VAT and GST on software
SaaS is taxable in a large share of US states and subject to VAT or GST on digital services in the UK, EU, Canada and Australia, each with its own registration threshold. We track taxable sales by jurisdiction, configure Stripe Tax, Avalara or TaxJar where you use them, and prepare filing workpapers for your tax adviser. We do not provide tax advice or file returns; your adviser or registered agent does.
SaaS metrics and investor reporting
MRR, ARR, gross and net churn, net revenue retention, CAC payback and burn multiple are reported from reconciled billing and ledger data with definitions documented. Board decks, lender covenant reports and data-room packs use the same figures as the monthly close, so nothing needs restating at the next round.
SaaS software we work in
- QuickBooks Online
- Xero
- Stripe
- Brex
- Ramp
- Gusto
- NetSuite
- Sage Intacct
- Avalara
- Chargebee
- Recurly
- Maxio
- All 50 platforms
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Frequently asked questions
Why does invoice status in Chargebee or Stripe need updating when a wire arrives?
Because the billing system drives dunning and access. If a wire is applied in the ledger but the invoice stays open in the billing system, the customer may receive reminders or lose access for an invoice they paid. We record the payment in both places on the same day so collections, revenue recognition and customer experience agree.
How do you handle a customer paying several invoices with one wire?
The remittance advice or AP portal shows which invoices the payment covers, and we apply the amount across them. Without a remittance we match by amount and customer, then ask the customer's AP contact in your name if anything is unclear. The payment sits in a clearing account, visible on the weekly note, until it is applied.
What happens when a customer short-pays a usage invoice?
The paid portion is applied and the shortfall is logged with the customer's stated reason, usually a disputed usage quantity. The account manager decides whether to credit or defend the charge; a credit note closes the balance and the revenue is adjusted, a defended charge moves to DunningDesk. Either way the invoice is never marked fully paid when it is not.
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