Quick comparison
Shortlist first, details second. Always double-check current pricing and plan limits on the vendor site.
| Tool | Best for | Setup time | Pricing | Why it’s here | Watch-out |
|---|---|---|---|---|---|
| FreshBooks Top pick | Service invoicing | 1–3 hours | Varies by plan | Client-friendly | Not deepest accounting |
| Xero | Accounting + invoicing | 1–2 days | Varies by plan | Strong accounting | More setup |
| QuickBooks Online | Mainstream standard | 1–2 days | Varies by plan | Broad ecosystem | Can feel complex |
How we picked
- Optimized for agency workflows: delivery visibility, client collaboration, and handoffs.
- Prioritized fast setup and simple ownership/permissions (so you actually adopt it).
- Checked integrations and reporting (so you don’t build a spreadsheet on the side).
- Included a clear watch‑out for each option to avoid bad fits.
We refresh guides when pricing/features shift. Always verify current terms on the vendor site.
FreshBooks — best for small agencies who want invoicing to be painless
Where it shines
- Service-friendly invoices and client experience
- Good for retainers and simple project billing (check plan details)
- Often a quicker setup than full accounting suites
Common gotchas
- check current fees and plan limits
- If you need deep accounting, you may outgrow it
Pick it if…
- You want clean invoicing and getting paid faster
- You’re a small team and value simplicity
Skip it if…
- You need full accounting workflows and heavy reporting
Xero — best if you want proper accounting with a clean UI
Where it shines
- Strong accounting foundation (check plan details)
- Good for agencies that want invoicing + bookkeeping in one
- Plays well with accountants (varies by region)
Common gotchas
- Setup takes longer — plan for it
- May require accountant input to do it right
Pick it if…
- You’re ready to treat accounting as a system, not a spreadsheet
- You want invoicing and bookkeeping together
Skip it if…
- You only want basic invoices and nothing else
QuickBooks Online — best for broad compatibility and ecosystem
Where it shines
- Common choice for many small businesses
- Strong integrations ecosystem (check plan details)
- Often easy to find accountant support
Common gotchas
- Can feel complex if you only need invoicing
- Pricing/tiers vary — verify before committing
Pick it if…
- You want a widely used standard and deep features
- You care about compatibility with other tools/accountants
Skip it if…
- You want a lightweight invoicing-only experience
Bottom line
If you mainly want to invoice clients cleanly, start with FreshBooks. If you’re serious about accounting, Xero is a strong foundation. If ecosystem and broad compatibility matter most, QuickBooks Online is the safe default.
FAQ
What’s the best invoicing software for a small agency?
Start with the Top pick in the quick comparison, then sanity‑check the watch‑out against your workflow and budget.
How long does it take to set up invoicing software?
Most teams can get a workable setup in a half day to two days. The real work is deciding your workflow (stages, ownership, and client touchpoints).
Do these tools support client access and permissions?
Usually, yes — but it varies by plan. Before committing, confirm guest seats, client permissions, and whether clients need paid accounts.