The Best Invoicing / Accounting Software for Agencies

Invoicing and accounting isn’t the exciting part of running an agency. But you notice immediately when your system is bad: invoices go out late, payments slip through, and your accountant sends you that email in March.

The answers in this thread were all over the map. Some agencies run everything through one platform. Others split invoicing and bookkeeping across two or three tools. A few have started building their own with AI. And almost everyone had a comment about price increases.

This post is a summary of a Tuesday Toolbox discussion inside The Admin Bar community, where agency owners shared what they use for invoicing and accounting, and what makes it work for them.

The Most Mentioned Invoicing & Accounting Tools

These tools came up repeatedly in the discussion:

• Zoho (Books, Invoice, and Zoho One)
• Xero
• QuickBooks Online
• Wave
• FreshBooks
• FreeAgent
• Invoice Ninja
• Agency CRMs with built-in invoicing

A number of other tools came up as well (we’ll get to those).

Why Agencies Choose These Invoicing & Accounting Tools

Zoho (Books, Invoice, and Zoho One)

The most-mentioned option overall, especially for agencies that want one platform to run everything.

Zoho showed up in a few forms: Zoho Books for full accounting, Zoho Invoice for invoicing only, and Zoho One as the bundle that adds CRM, projects, desk, and subscription billing. Taken together, it edged ahead of every other option in the thread.

“The first two absolutely run my business. I left QuickBooks when the pricing got crazy and have never looked back.”

Ben Shapiro

Ben runs Zoho Books and Zoho Billing (for hosting subscriptions) as the core of his business, with Desk, Projects, and CRM alongside them. Dee Davidson Zunker, Christina Varro, and Scott Gingrich are also on Zoho One.

Patrick Boehner has used Zoho Books for years and highlighted the pricing history: “It’s full-featured and priced in a way that’s hard to compare to many other options and they haven’t had huge price jumps in those years either.” Stacy M. Clements likes that it sends recurring invoices and reminders automatically, connects to her bank and credit card so she doesn’t enter expenses by hand, and can turn tracked time into an invoice.

Alex Celeste’s agency uses Zoho Invoice, partly because they were already in the Zoho ecosystem. They’ve considered moving to Stripe directly, but some clients still pay by check or through their own bill pay tools. Satoshi Fujita mentioned Wave or Zoho Invoice.

Best fit: agencies who want invoicing, accounting, subscriptions, and CRM in one stack, and who don’t want to watch prices jump every year.

Xero

Loyal users, a love-hate relationship with the interface, and a growing frustration with pricing.

Xero had a devoted following in the thread, much of it from outside the US. Stacey Watson has been on it since 2013. Sandy Forbes Taylor uses it with Xero Projects. Priscilla Morris summed up the user experience: “Xero, butt ugly, but it works fine for me.”

Karen Leslie, in Australia, stays on Xero for a specific structural reason: she runs two businesses through a Trust and can handle both in one Xero setup. She looked at alternatives but found them just as expensive or more so for two businesses. She also noted she can’t download a full backup, only exports.

The pricing complaints were the loudest here. Gen Herres wants to leave over annual increases, but needs accessibility in the bill pay process, which rules out nearly every alternative she’s looked at, and the migration would be its own project.

Best fit: agencies (especially outside the US) who want a well-established accounting platform and have a reason, such as multi-entity setups or an accountant who prefers it, to stay in the Xero ecosystem.

QuickBooks Online

The tool people use because their accountant does, not necessarily because they like it.

QuickBooks came up often, and the tone was telling. Several members use it with open reluctance.

“I don’t necessarily like QuickBooks but it made everything a lot easier.”

Troy Glancy

Troy’s story is worth reading closely. He’d used Square and other invoicing platforms for years, but kept running into the same problem: invoices lived in one place, money moved through multiple places, and everything still had to be reconciled in QuickBooks for his accountant. Moving back to QuickBooks and using his primary bank for deposits simplified the whole picture.

John Serbell pairs Moxie for invoicing with QuickBooks Online for accounting, and made his feelings about Intuit very clear. John Tully called it a “living hell” but says it’s been the go-to for every CPA he’s worked with. Jeremy Selph likes that it works on his phone, tablet, and PC. Tony White and Garrett Chris use it without elaboration.

Jean-Francois Arseneault takes a hands-off approach: Woo with Subscriptions captures payment (prepaid, by credit card), and QuickBooks plus an accounting firm handle the rest, “so we can focus on the business.”

Plenty of members have also left. Ben Shapiro went to Zoho over pricing. Jennifer Moss moved to Wave. Austin Siewert is planning to drop it.

Best fit: agencies whose accountant or bookkeeper requires it, or who want the most widely supported accounting platform and are willing to put up with the price and the interface.

Wave

The free-tier favorite that long-time users keep recommending.

Wave came up from several members who’ve been on it for years, and the free tier is the reason.

“I’ve been using the free tier for over 5 years and it’s worked great.”

George H Woodard III

George listed what he gets from it: invoicing (including recurring), payment links, bank reconciliation, accounting, expense tracking, and a mobile app. Becky McAllister and Paul Archer have also used the free tier for years. Jennifer Moss moved from QuickBooks to Wave and says it’s “fine,” saving “hundreds of dollars a year.” Camo Jones uses Xero for the business and Wave for personal.

Rachelle Wise splits the work: Plutio for invoicing, Wave for bookkeeping.

Best fit: solo operators and small agencies with straightforward needs who want solid bookkeeping without a monthly bill.

FreshBooks

Dependable for a long time, increasingly expensive.

FreshBooks was the clearest example of a tool people like but feel squeezed by. Nobody complained about reliability. Everyone complained about price.

“I’ve been using Freshbooks for years. Are there better/cheaper solutions, probably. It has never failed me in any way.”

Brett Atkin

“Love so many things about it. The fact that they keep raising prices is NOT one of those things.”

Bj Bowen

James Rice has been on it for almost 20 years on a cheap legacy plan, which is its own kind of loyalty story. Mark Collard is thinking about moving because it’s “getting a bit pricey.” Todd Chaney is happy but says it “gets expensive fast,” and has considered writing his own app with AI.

Best fit: agencies on legacy pricing who want invoicing and time tracking that just works. For new signups, the pricing conversation in this thread is worth considering first.

FreeAgent

The UK pick, and one with a clever bundling advantage.

FreeAgent came up from two UK-based members, and both mentioned that it comes free with certain business bank accounts.

“I love the ability to set up recurring invoices. Their support is also really helpful and I get answers (not more questions) back within a day.”

Kristen Sousa

Alison Donnellan used to pay for it directly, then found it’s included with NatWest or Mettle business accounts. One catch: it’s one business per FreeAgent account, so her second business needed a separate NatWest account to qualify. She also pointed out that FreeAgent works well with assistive technology, and that her father, a Chartered Accountant who was previously a Sage user, now prefers it.

Best fit: UK-based agencies and freelancers who want a clean, well-supported accounting tool, ideally bundled free through their business bank.

Invoice Ninja

The open-source option for people who want control.

Invoice Ninja came up from three members, including one who self-hosts it.

Asing De Naam and Nick Bostic both use it (Nick self-hosted). Marty Kendrick McIntyre uses it for invoicing and Manager.io for accounting, and hasn’t yet tried the invoicing features built into Manager.

Best fit: technically comfortable agencies who want an open-source, self-hostable invoicing tool and don’t mind managing it.

Agency CRMs with built-in invoicing

Several members don’t use a dedicated invoicing tool at all. They invoice from the same platform that handles proposals, contracts, and client management.

• Moxie: Joel McDonald pairs it with Excel and says “actual accounting services have become too pricey for what I need.” John Serbell uses it for invoicing and QuickBooks for accounting.
• HoneyBook: Brian Schnurr and Jacob Householder use it for quotes, invoices, and contracts. Jacob adds WHMCS for SaaS invoicing.
• Dubsado: John Catherall uses it for invoicing, with Pandle for accounting.
• 17hats: Gaye Nilson has used it for years for quoting, invoicing, recurring invoices, and workflows. She finds bookkeeping and reporting basic and reconciles manually. She’s grandfathered into older pricing and notes it’s expensive now.

The upside is one flow from proposal to contract to invoice. The downside, as Gaye’s comment shows, is that accounting depth is usually limited, so most of these members still need something else for the books.

Best fit: solo and small agencies who value a single client-management flow over deep accounting features.

Notable Mentions

These also came up in the thread:

• Tillage (Austin Siewert, Danny Ferry): Both use it with an MCP for generating estimates quickly, and Austin says he’s saving thousands on Stripe fees. Austin banks with Mercury, which recently added bookkeeping, and will likely drop QuickBooks.
• Plutio: Rachelle Wise uses it for invoicing alongside Wave
• WHMCS: Valerie Jean used it for hosting and domain subscriptions, but has since scaled down and moved to Stripe invoicing, which she finds “a bit clunky so far”
• Blesta and Puzzle.io: Rob Marlbrough uses Blesta for invoicing and subscriptions with provisioning and suspension of server accounts, and Puzzle for accounting
• Rounded: Tracey Harrison’s pick in Australia, built for sole traders
• LiteBooks: Eoin Healy uses it in Ireland; it’s made for Irish businesses
• Elorus: Irene Koukia uses it because Greek invoicing involves digital signatures and other complexity. It’s available worldwide.
• Cobalt: Matt Hancock uses it in New Zealand for invoicing and expense tracking, and likes that the developer takes feedback on board
• PerfexCRM: Patrick van Elk uses it for invoicing, and LibreOffice Calc to deliver data to his accountant
• Subtotal and WorkingHours: Christian Strasser uses the pair for a one-time payment of $10
• Fygaro, OneSuite, Rhino: each mentioned once, without much detail

The Price Increase Problem

If there was one shared frustration in this thread, it was pricing.

FreshBooks users described it as getting expensive fast. Xero users described annual increases. 17hats users are grandfathered into older pricing and know it. Ben Shapiro left QuickBooks entirely when pricing got “crazy.”

Gen Herres offered the most practical advice in the thread: before committing to any platform, look at its pricing page over the last few years. Many of these tools have raised prices every single year. That’s a better predictor of what you’ll pay in year three than today’s sticker price.

The trap she described is also worth noting. Once your books, bill pay, and history live in a platform, leaving gets harder every year, which is why legacy plans (like James Rice’s FreshBooks) and free tiers (like Wave’s) came up so often as reasons to stay put.

Patterns We Noticed

A few things stood out across the thread:

• Price increases are driving real migration. Zoho, Wave, and a handful of newer tools are picking up members who left QuickBooks, FreshBooks, or Xero. Most of the people complaining aren’t leaving yet, but they’re watching their renewal dates.
• “My accountant uses it” is a legitimate reason. Several QuickBooks users made it clear it’s not a preference, it’s a workflow requirement. If your accountant or bookkeeper works in a specific tool, that matters more than any feature comparison.
• Fewer places for money to live means fewer headaches. Troy Glancy’s story about reconciling across invoicing tools, bank accounts, and QuickBooks is a pattern worth heeding. The more places money moves through, the more reconciliation work you create for yourself.
• Location shapes the right answer. FreeAgent (UK), Xero (AU/NZ), Rounded (AU), Cobalt (NZ), Elorus (Greece), and LiteBooks (Ireland) all came up for compliance or local-banking reasons. US-centric advice doesn’t always travel.
• Invoicing and accounting are often separate decisions. Many members run one tool for invoicing and another for accounting: Moxie plus QuickBooks, Dubsado plus Pandle, Plutio plus Wave, Invoice Ninja plus Manager.io.
• Some agencies are building their own. Mark Szymanski built a custom setup inside his own AI operating system, pulling transaction history through SimpleFIN and sending invoices through Stripe, all orchestrated by Claude Code. Todd Chaney is considering something similar. Austin Siewert’s Tillage-plus-MCP setup points the same direction. It’s early, but it’s no longer fringe.
• Not everyone can pay by card. Alex Celeste noted a few clients still insist on checks or their own bill pay tools, which is why Stripe-only isn’t an option for them yet.

How to Choose the Right Invoicing & Accounting Software

These questions can help narrow it down:

• Does your accountant or bookkeeper require a specific platform?
• Do you need invoicing only, or full accounting with bank reconciliation and reports?
• Do you want everything in one system (Zoho One, HoneyBook), or best-of-breed tools for each job?
• Where are you based? Local tax, compliance, and banking integrations vary a lot.
• Have you checked the platform’s price history, not just today’s price?
• Do you bill for recurring services like hosting and care plans? If so, how well does the tool handle subscriptions and reminders?
• Do all your clients pay by card, or do some need checks, bank transfers, or their own bill pay systems?

Frequently Asked Questions About Invoicing & Accounting Software for Agencies

What is the best invoicing software for web agencies? It depends on whether you want invoicing alone or a full accounting platform. In this community, Zoho (Books, Invoice, or Zoho One) was the most mentioned, followed closely by Xero, QuickBooks Online, and Wave. For invoicing tied to proposals and contracts, Moxie, HoneyBook, and Dubsado came up.

Is there a free accounting tool for freelancers and small agencies? Several members have used Wave’s free tier for years for invoicing, recurring invoices, bank reconciliation, and expense tracking. Mettle and NatWest business accounts in the UK can also come with FreeAgent included. Invoice Ninja is open-source and can be self-hosted.

What are the best QuickBooks alternatives? Members who left QuickBooks mostly went to Zoho Books or Wave, usually over pricing. Others moved to Xero or, in Austin Siewert’s case, are exploring Mercury’s built-in bookkeeping and Tillage. If your accountant requires QuickBooks, that may outweigh the cost.

Should I use separate tools for invoicing and accounting? Many agencies do. A common pattern is a client-facing invoicing tool (Moxie, Dubsado, Invoice Ninja, Plutio) paired with a dedicated accounting platform (QuickBooks, Wave, Pandle, Manager.io). The trade-off, as Troy Glancy found, is that you have more reconciliation to do when money passes through several places. One platform can be simpler, as long as it covers what you need.

What should I use if I’m outside the US? Local compliance matters. This thread had FreeAgent for the UK, Xero for Australia and New Zealand, Rounded for Australian sole traders, Cobalt in New Zealand, LiteBooks for Ireland, and Elorus for Greece, where invoicing requirements can be complex. Check that any tool you consider supports your country’s tax and invoicing rules.

Are accounting software prices going up? Based on this thread, yes. Members reported regular increases from FreshBooks, Xero, QuickBooks, and 17hats. One member’s advice: review a platform’s pricing page over the last few years before committing, since past increases are a good indicator of future ones.