Guide
Best Accounting And Invoicing Software for Agencies (2026)
By Red Kite Search Agency Created Updated 8 min read
Summary
Xero is the best accounting platform for agencies; QuickBooks is the best if your accountant uses it; Harvest is the best for time-based billing; Bonsai is the best for freelancers and tiny studios. Prices and ratings were checked in October 2026 and change often.
What are the best accounting and invoicing software for agencies in 2026?
Agencies need to send invoices, get paid, and show a profit, and the right tool depends on whether you need a full accounting ledger or mainly invoicing tied to tracked time. The four tools here cover that range.
We compared two full accounting platforms with two lighter tools built around time and client paperwork. Most agencies end up using one ledger, and often one lighter tool next to it.
Our shortlist, in order: Xero, QuickBooks, Harvest, Bonsai. The table puts them side by side.
| Tool | Best for | Editorial score | Review-site ratings | Pricing |
|---|---|---|---|---|
| Xero | Best accounting platform for agencies | 4.1 / 5 | G2 4.4 | Early $27, Growing $59, and Established $97 per month, with no per-user fees. New customers see a steep discount for the first 3 months. |
| QuickBooks | Best if your accountant uses it | 3.9 / 5 | G2 4 | 30-day free trial. Regular monthly prices: Simple Start $38, Essentials $85, Plus $140, and Advanced $340 per month. New customers see 50% off for the first 3 months. |
| Harvest | Best for time-based billing | 4.1 / 5 | G2 4.3, Capterra 4.3 | Free for 1 seat. Teams $9 and Enterprise $14 per seat per month (billed annually). |
| Bonsai | Best for freelancers and tiny studios | 3.9 / 5 | Capterra 4.6, G2 4.3, Trustpilot 4.5 | 7-day free trial. About $9-$49 per user per month on annual billing (Basic to Elite). |
How did we choose the best accounting and invoicing software?
We included tools with public pricing, substantial review-site evidence, and clear use among agencies and freelancers. Pricing and features come from vendor pages, and ratings come from G2.
We separated ledgers from invoicing tools in our write-ups, since they answer different questions. Scores reflect fit for agencies serving several clients.
What we looked for
- Whether it is a full ledger or an invoicing and time tool.
- Pricing model: per user, per plan, or per seat, and the regular price after promotions.
- Project time and cost tracking, and multi-currency support.
- Accountant collaboration and integrations.
- Published security and support evidence.
- Public evidence: review-site ratings and review counts.
Is Xero a good accounting or invoicing tool for agencies?
Best accounting platform for agencies: Xero charges no per-user fees, has more than 1,000 app integrations, and states SOC 2, ISO 27001, and PCI DSS compliance. Project tracking and multi-currency are on the top plan, and support is online-first.
Xero is cloud accounting software for invoicing, bills, bank reconciliation, reporting, and cash flow forecasting, with more than 1,000 app integrations. Plans have no per-user license fees, and project time and cost tracking and multi-currency start on the top plan.
Who it suits: Agencies that want a well-integrated ledger without paying per user, and work with international clients.
Xero pros
- No per-user license fees on any plan.
- More than 1,000 app integrations.
- SOC 2 reports, ISO/IEC 27001:2022 and PCI DSS compliance stated.
- Higher G2 rating than QuickBooks Online.
Xero cons
- Early caps invoices at 20 and bills at 5 a month.
- Project time and cost tracking and multi-currency are only on Established.
- Chargeable direct bank feeds can add usage costs.
- Support is online-first, with no phone or email stated and no response times.
Is QuickBooks a good accounting or invoicing tool for agencies?
Best if your accountant uses it: QuickBooks is the most widely used ledger among accountants, with free accountant access and project profitability from Plus. Regular prices double after a 3-month promotion, and plans cap users.
QuickBooks Online is cloud accounting software for invoicing, expenses, bank reconciliation, reports, bill pay, and tax tools, with AI features and a large app marketplace. Plans are priced per month for a set number of users, and project profitability starts on Plus.
Who it suits: Agencies that need full bookkeeping and tax-ready accounts, and whose accountant already uses QuickBooks.
QuickBooks pros
- The most common accounting tool among accountants and bookkeepers.
- Free accountant access, with 2 or 3 accountants included.
- A large app marketplace and AI features for categorizing and reconciling.
- Project profitability on Plus and Advanced, with a 30-day free trial.
QuickBooks cons
- Regular prices are about double the promotional price shown for the first 3 months.
- Each plan limits users: 1 on Simple Start, 3 on Essentials, 5 on Plus, 25 on Advanced.
- Project profitability needs Plus; time tracking plan inclusion is not clearly stated.
- G2 reviewers rate it lower than Xero and FreshBooks.
Is Harvest a good accounting or invoicing tool for agencies?
Best for time-based billing: Harvest turns tracked time and expenses into invoices, with a free plan, a strong timer, and accounting integrations. It does not replace a ledger.
Harvest tracks time and expenses and turns them into invoices, with a mobile timer and a large integration list. Profitability reports and timesheet approvals sit on the Enterprise plan.
Who it suits: Freelancers and small to mid-size agencies that bill by time or project and want tracking and invoicing in one product.
Harvest pros
- Simple, quick timer and manual entry, plus a well-liked mobile app.
- Time, expenses, and invoices live together, so billing is fast.
- Integrations with Asana, Basecamp, Slack, and QuickBooks.
- Free plan for one seat and two projects.
Harvest cons
- Reporting is less flexible than some agencies need, so many export to a spreadsheet.
- Profitability reporting and timesheet approval require the Enterprise plan.
- Accounting and payment integrations start on the Teams plan.
- Permissions and recurring-entry options are limited.
Is Bonsai a good accounting or invoicing tool for agencies?
Best for freelancers and tiny studios: Bonsai bundles proposals, contracts, time tracking, invoices, and basic accounting in one tool. It is light on team features, and reviewers report payment holds.
Bonsai bundles the paperwork a solo operator needs: proposals, contracts, time tracking, invoices, payments, and basic accounting. It is aimed at freelancers and very small studios.
Who it suits: Freelancers, consultants, and tiny agencies that want one tool for the client paperwork cycle.
Bonsai pros
- Contract templates and invoicing save time on admin.
- Time tracking is included on every plan.
- Priced per user with a 7-day trial, and cheaper than assembling several tools.
- Unlimited clients on all plans.
Bonsai cons
- Invoicing, contracts, and accounting are not in the cheapest Basic tier.
- Reviewers report payment holds and support delays.
- Tax features cost extra, and plan prices rose for some users.
- Light on project management and team features for larger agencies.
How much do the best accounting and invoicing software cost?
Pricing models differ, so compare totals. Xero charges by plan with no per-user fees, QuickBooks charges by plan with user limits, and Harvest and Bonsai charge per seat or user. Both ledgers discount the first three months, so budget with the regular price.
| Tool | Plan | Price | What stands out |
|---|---|---|---|
| Xero | Early | $27 per month (monthly billing) | Quotes and 20 invoices, 5 bills, bank reconciliation, 30-day cash flow forecast |
| Xero | Growing | $59 per month (monthly billing) | Unlimited invoices and quotes, automated bill entry, dashboards, budgets, 60-day cash flow forecast |
| Xero | Established | $97 per month (monthly billing) | Multiple currencies, project time and cost tracking, expense claims, analytics, 180-day cash flow forecast |
| QuickBooks | Simple Start | $38 per month (monthly billing) | 1 user plus 2 accountants, invoicing, expense categorization, automated bill pay with free ACH, AI chat |
| QuickBooks | Essentials | $85 per month (monthly billing) | 3 users plus 2 accountants, bulk invoicing, Payments AI, quarterly tax estimates, enhanced reports |
| QuickBooks | Plus | $140 per month (monthly billing) | 5 users plus 2 accountants, project profitability, budgets, inventory, classes and locations (up to 40) |
| QuickBooks | Advanced | $340 per month (monthly billing) | 25 users plus 3 accountants, advanced project financials, custom permissions, workflow automation, priority support |
| Harvest | Free | $0 | 1 seat, 2 projects |
| Harvest | Teams | $9 per seat/month (annual billing); $11 monthly | Team reports, accounting and payment integrations |
| Harvest | Enterprise | $14 per seat/month (annual billing); $17.50 monthly | Profitability, approvals, SSO, unlimited custom reports |
| Harvest | Enterprise Plus | Custom | Custom terms |
| Bonsai | Basic | $9 per user/month (annual billing); $15 monthly | Time tracking, unlimited clients |
| Bonsai | Essentials | $19 per user/month (annual billing); $25 monthly | Invoices, payments, proposals, contracts |
| Bonsai | Premium | $29 per user/month (annual billing); $39 monthly | Gantt view, deals pipeline, profit reports |
| Bonsai | Elite | $49 per user/month (annual billing); $59 monthly | Custom permissions, timesheet locking, 3 user minimum |
What do reviewers say about these accounting and invoicing software?
G2 evidence is solid for all four. QuickBooks has the largest base but a lower score, Xero and Harvest are well rated with large bases, and Bonsai is well rated on a smaller base. Scores are close, so use trials to separate them.
| Tool | Source | Rating | Number of reviews |
|---|---|---|---|
| Xero | G2 | 4.4 / 5 | 1,609 |
| QuickBooks | G2 | 4 / 5 | 3,827 |
| Harvest | G2 | 4.3 / 5 | 843 |
| Harvest | Capterra | 4.3 / 5 | 367 |
| Bonsai | Capterra | 4.6 / 5 | 95 |
| Bonsai | G2 | 4.3 / 5 | 101 |
| Bonsai | Trustpilot | 4.5 / 5 | 639 |
Reviewer themes for Xero
- G2 shows Xero at 4.4 from 1,609 reviews.
- G2 reviewers praise unlimited users, extensive integrations, and bank reconciliation automation.
Reviewer themes for QuickBooks
- G2 shows QuickBooks Online at 4 from 3,827 reviews.
- G2 comparison data rates Xero higher than QuickBooks Online.
Reviewer themes for Harvest
- G2 shows Harvest at 4.3 from 843 reviews, and Capterra shows 4.3 from 367 reviews.
- Capterra reviewers describe the interface as easy to learn and call the timer and manual entries straightforward.
Reviewer themes for Bonsai
- Capterra shows Bonsai at 4.6 from 95 reviews, G2 at 4.3 from 101, and Trustpilot at 4.5 from 639.
- Reviewers value an all-in-one tool that covers the freelance business cycle.
How do you choose the right accounting or invoicing tool for your agency?
Start by deciding whether you need a ledger. If your accountant uses a particular one, that usually settles it, and a lighter tool can sit alongside.
Whichever you shortlist, run a trial with a real month of invoices and ask your accountant to look at the output.
A quick decision guide
- A full ledger with no per-user fees: Xero.
- A ledger your accountant already uses: QuickBooks.
- Time tracking that turns into invoices: Harvest.
- One tool for freelancer paperwork: Bonsai.
- Both a ledger and time tracking: Xero or QuickBooks with Harvest.
Frequently asked questions
- What is the best accounting software for agencies?
- Xero for no per-user fees, or QuickBooks if your accountant already uses it.
- Do I need accounting software and a time tracker?
- Often yes. A time tracker such as Harvest captures billable hours, and the ledger records the money.
- Which tool is cheapest?
- Harvest has a free plan and low paid prices, and Bonsai has a low entry price.
- Which tools have a free plan?
- Harvest has a free plan for one seat and two projects.
- How were the tools rated?
- Ratings come from G2, and the editorial scores are our own judgement of fit for agencies.
Sources
Prices, plan limits, and ratings were gathered in October 2026 from:
- Xero pricing page
- QuickBooks pricing page
- Harvest pricing page
- Bonsai pricing page
- G2