How to Track Partial Payments on Invoices as a Freelancer

When do freelancers deal with partial payments?

Partial payments are more common than most freelancers expect. They happen in several scenarios:

• Deposits and upfront payments— you agree on 50% upfront before starting the work. The client pays half, and the remaining half is due on delivery. Until both halves land, the invoice is partially paid.
• Milestone billing— larger projects are often split into phases. A design project might have three milestones: wireframes, mockups, and final delivery. Each milestone triggers a partial payment against the total invoice.
• Client budget constraints— sometimes a client simply can't pay the full amount at once. They pay what they can now and the remainder later. This is more common with small businesses and startups.
• Disputed amounts— the client agrees with most of the invoice but disputes one line item. They pay the undisputed portion while you sort out the rest.
• Retainer drawdowns— if a client pays a monthly retainer and you invoice for additional work, they might offset part of the invoice against the retainer balance.

In every case, you need a clear record of what was paid, when, and how much remains outstanding. A simple “paid / unpaid” toggle won't cut it.

How to record a partial payment in Bontello

Recording partial payments should be fast and leave a clear audit trail. Here's how it works in Bontello's invoice history:

1. Open the invoice from your history or dashboard.
2. Click Record Payment. Enter the amount received (e.g., €1,500 out of €3,000).
3. Add the payment date and an optional note (e.g., “First milestone — wireframes delivered”).
4. Save. The invoice status automatically updates to Partially Paid, and the remaining balance is calculated.
5. When the next payment arrives, repeat the process. Once the total paid equals the invoice amount, the status flips to Paid.

Every payment is logged with a timestamp, so you have a complete payment history for each invoice. This is essential for tax reporting and for resolving any disputes with clients.

Understanding invoice statuses

A clear status system prevents confusion. Here's how Bontello tracks invoice lifecycle:

Notice that Overdue can apply to both fully unpaid and partially paid invoices. If a client paid half but the due date passes before the second half arrives, the invoice is overdue for the remaining amount.

Tracking remaining balance and payment history

Every invoice with partial payments should show two things at a glance: the total paid so far and the remaining balance. In your dashboard, partially paid invoices appear in their own section so you never lose sight of money that's still owed to you.

The payment history for each invoice acts as a mini-ledger:

This level of detail matters when tax season arrives. Your accountant (or your own VAT return) needs to know exactly when money was received, not just that it was received eventually.

Using payment terms to structure deposits

The best way to handle partial payments smoothly is to build them into your quotes and contracts from the start. Common structures for freelancers:

• 50/50 split— 50% upfront, 50% on delivery. The simplest structure and works well for projects under €5,000.
• 30/30/40 split— 30% upfront, 30% at midpoint, 40% on final delivery. Better for larger projects where the risk is higher.
• Monthly billing— for retainers or ongoing work, invoice at the end of each month. Each invoice covers that month's work only.

State the payment structure clearly on your quote and contract. When the client signs, they've agreed to the schedule — which makes follow-up much easier if a payment is late.

Late payment interest on partial balances

Under the EU Late Payment Directive (2011/7/EU), you can charge interest on overdue B2B invoices at the ECB reference rate + 8 percentage points. This applies to the outstanding balance, not the original invoice total. If a client paid half on time but the other half is 30 days late, you calculate interest only on the unpaid portion.

You're also entitled to a flat €40 recovery fee per overdue invoice. While most freelancers don't enforce this, mentioning it in your payment reminders can speed things up.

Key takeaways

• Partial payments happen with deposits, milestones, budget constraints, and disputed amounts.
• Record every payment with the amount, date, and a note — build a mini-ledger per invoice.
• Use clear statuses: Draft → Sent → Partially Paid → Paid (or Overdue).
• Track remaining balances on your dashboard so nothing slips through the cracks.
• Structure deposits in your quotes upfront — 50/50 or 30/30/40 splits are standard.
• EU late payment interest applies to the outstanding balance, not the full invoice total.