Both products deserve a look when you want to run invoicing on your own server. The sharper decision is what must happen around the invoice. A business that needs tracked time, customer logins and payment-gateway collection has different requirements from one billing fixed-price milestones and recording bank transfers.
Invoice Ninja's official guide documents time tracking, recurring invoices, a client portal and online payment gateways. Its self-hosting site also offers a hosted alternative. Those are material options to test if the workflow needs them. Sources checked 8 October 2026: Invoice Ninja user guide and self-hosting overview.
Compare one real job
| Need | Pepper | What to test in Invoice Ninja |
|---|---|---|
| Fixed-price stages | Versioned agreed scope, milestone approval and linked invoice drafts | How your agreement and billing stages fit its projects and invoices |
| Time-based billing | Timers, weekly timesheets and invoice drafts from grouped, rounded time | Its documented time and task workflow |
| Customer access | Signed document links; no customer login portal | The documented client portal and its permissions |
| Receiving money | Staff record money received elsewhere | Your preferred gateway, available methods and provider fees |
| Hosting | Your installation and database | Self-hosted or hosted service |
Take a EUR 3,600 website job with design and build stages. In Pepper, agree two fixed-price milestones, approve completed work and prepare the exact invoice draft. If you charge for every recorded hour and want the client to pay in a portal, test that full journey in Invoice Ninja before choosing.
Pepper also supports manual purchases with receipt attachments and monthly, quarterly and yearly exports for an accountant. It has no bookkeeping ledger, bank feed or automatic expense rebilling. A project cost link records the connection without adding it to the client's invoice.
Compare source rights and ongoing work
Invoice Ninja describes its self-hosted code as source available and publishes separate license and self-hosting terms. Check the permitted use and branding conditions for your installation. Invoice Ninja source and hosting information, self-hosting terms.
Pepper costs $199 for one production installation, including full source, a perpetual licence, and one year of updates and support. Updates and support renew automatically at $199/year unless you cancel. Cancel anytime to stop future charges; your downloaded copy keeps working after the paid period ends. Hosting and maintenance remain your responsibility. The license terms define the source-use limits.
Before switching
Try a quote, an invoice correction and your accountant's hand-off. Confirm who maintains the server and any custom code. Pepper has no Invoice Ninja migration tool, so retain the original system and its records while planning the move.
Start with the worked milestone invoice to check Pepper’s fixed-price workflow. Use an installed test copy for writes; the public demo is read-only. The ownership guide explains source rights and maintenance.