How does a deposit become a payment on an invoice?

Invoice Ninja’s Transactions screen can show a bank deposit and suggest a matching invoice. A suggested match can wait for your confirmation. Read the linked invoice and amount before accepting it. The hosted plans list automatic bank feeds from Enterprise. The documentation also covers importing a bank CSV.

What changes if you run Invoice Ninja yourself?

The hosted Free plan lists five clients and unlimited invoicing. Self-hosted has a separate setup and terms. Your team handles the server, backups and upgrades. Export the data you need and check that invoice and attachment copies are included in your handoff before switching.

Can you tell which fictional client actually paid?

Draw two invoices with the same amount and a deposit with a reference for just one invoice.

Read more than the amount
Use the reference to choose one candidate. Leave the other open.
Plan what to carry
Mark the invoice number, client, matching payment and any document copies needed to explain the result.