How to choose and implement the right bookkeeping software

Thousands of businesses struggle with their bookkeeping. Currently in Australia, 80% of SMBs rely on spreadsheets, and many more are spending each day fighting a software platform that doesn’t fit their business’s needs.

While choosing the right bookkeeping software might seem like a simple choice, the reality is that if you choose the wrong one, it can chew up the time you could be spending focusing on your business or lead to accidental compliance mistakes.

It’s not all doom and gloom, though. There are a bunch of quality options on the market that will help transform your financial operations. In this article, we’re going to help you identify the right system for your unique business.

A checklist for choosing the right bookkeeping software

Let’s get straight into what you need to keep in mind when shopping around for bookkeeping software. We recommend that you check vendors’ websites, trusted review sites like Capterra or G2, and schedule a time to talk with their sales team.

Here are some considerations you may want to include in your new bookkeeping software checklist:

Compliance support

• [ ] Supports STP Phase 2 directly or via a reliable payroll integration (a must-have for payroll in Australia)
• [ ] Built to handle GST, including BAS reporting
• [ ] Updated regularly to reflect ATO rule changes
• [ ] Allows you to lock reporting periods to prevent accidental changes

Connected bank feeds and reconciliation

• [ ] Has a connection to Australian banks
• [ ] Provides a clear audit trail
• [ ] Allows for automated feeds rather than manual imports
• [ ] Makes reconciliation simple, with clear matching and error flags
• [ ] Supports automations for recurring transactions

Invoices and quotes

• [ ] Creates professional invoices and quotes
• [ ] Allows you to make custom invoice and quote templates
• [ ] Converts quotes to invoices easily
• [ ] Supports recurring invoices and online payments
• [ ] Supports multi-currency transactions
• [ ] Tracks overdue invoices and customer balances

Payroll workflows

• [ ] Includes payroll or integrates cleanly with payroll software
• [ ] Supports superannuation, leave balances, and pay conditions
• [ ] Sends STP reports to the ATO without manual intervention

Inventory or billable hour management

• [ ] Tracks stock levels accurately (if you sell products)
• [ ] Supports job or project costing (if you sell services)
• [ ] Handles cost allocation without workarounds
• [ ] Provides basic profitability reporting

Usability and pricing

• [ ] Allows multiple users with different permission controls
• [ ] Includes accountant or bookkeeper access at no extra cost
• [ ] Has transparent pricing, including add-ons
• [ ] Can scale as your team or transactions grow

You may not need all of these requirements for your business, so pick and choose what matters most to your team. Once you have your shortlist of requirements, check it over with people in your business who will need to access the software to ensure you haven’t missed any key details.

The 5 best bookkeeping software options

The bookkeeping software you choose can either add hurdles to your day or quietly do its job in the background. These five platforms are the ones we see clients successfully using most often. Each helps reduce errors, simplify day-to-day bookkeeping, and give you faster, more reliable financial reporting.

An overview of the top 5 options

1. Xero

Xero is the market-leading software platform for Australian small to mid-sized businesses. It’s great if you want simple, cloud-based bookkeeping that you can integrate with other platforms.

The platform covers all your essentials well, including invoicing, bank feeds, expense tracking, and reporting, all in one place. It’s also easy to access from anywhere, works across desktop and mobile app, and allows you to share access with your accountant.

Xero’s features, like automated reminders, transaction matching, and customisable dashboards, help reduce manual work and give you confidence in your numbers.

“Xero is very easy to use and adaptable for all types of businesses. It provides quick access to favorites and allows dashboards to be customised for each user. Overall, I’m very happy with the system.”, Xero Capterra review

2. MYOB

MYOB has been around since 1991, and since it’s a long-established platform, most accountants have experience using it. The MYOB software is a good fit for small to mid-sized businesses that need a more structured, all-in-one system.

The platform covers all your core accounting functions, including invoicing, bank reconciliation, payroll, and accounts payable and receivable. They also offer detailed reporting and permission settings, which can be useful as teams grow or financial complexity increases.

“I enjoy working with this product as it has streamlined some work for my clients and I along with complying with legislative requirements.”, MYOB Capterra review

3. QuickBooks

QuickBooks is a strong option for midsize to large businesses that need more advanced accounting features and tighter controls. It’s a great option for businesses managing lots of transactions and users.

Businesses use QuickBooks for easy invoicing, expense tracking, inventory management, and reporting. Its extra features, like customisable reports, secure user permissions, and dashboards, are great for giving businesses a better view of their finances. The only drawback is that its setup and ongoing costs can be higher than simpler bookkeeping tools.

“Good workflow, easy to use and minimal glitches. I really like that you can manage inventory, create purchase orders, sales orders and invoices in the same place.”, QuickBooks Capterra review

4. Reckon

Reckon is a good option for small businesses that want a simple, affordable bookkeeping platform without paying for features they don’t need. It’s particularly well-suited to sole traders and small teams looking for basic accounting tools at a lower cost than larger platforms.

Small businesses like it for its no-nonsense invoicing, online access, and reporting. Its modular setup and competitive pricing make it appealing for businesses that want flexibility, while many users say that it offers great customer support.

“All very easy to use and the staff are always helpfull when I need help.”, Reckon Capterra review

5. Zoho Books

Zoho Books is a good fit for small to mid-sized businesses that want affordable, cloud-based bookkeeping, especially if they already use other Zoho products.

Zoho Books covers the core accounting basics, including invoicing, recurring billing, bank reconciliation, expense tracking, and reporting, all managed from a single dashboard. Businesses also value its pricing (including a free plan for micro businesses), and how smoothly it connects with tools like the wider Zoho ecosystem.

“Zoho Books is an excellent option for your company’s bookkeeping and accounting. Invoicing and billing is done in the dashboard, reporting on income, expenditure and payables are separated and even financial reconciliations can be actioned automatically.”, Zoho Books Capterra review

How to set up bookkeeping software

Once you’ve decided what software you’re going to use, here is a simple process you can follow to get it set up.

1. Input the basics

Start by entering your business details into the software. This usually includes your business name, ABN, and whether you’re registered for GST.

Next, you’ll need to choose how you want the software to handle GST. You’ll usually see two options:

• Cash basis: GST is counted when money actually hits your bank account (or when you pay a bill).

• Accrual basis: GST is counted when you send or receive an invoice, even if the money hasn’t moved yet.

If you’re not sure which one applies to you, check your last BAS or ask your accountant.

2. Set up your chart of accounts

Your chart of accounts is a list of categories your money gets sorted into, like income, rent, software, wages, equipment, and more.

Most modern systems will come with these already set up, and in most cases, you should leave them as they are. Keep in mind that adding too many custom categories early on can confuse things, not make them clearer.

3. Add your opening balances

Opening balances tell the software where your finances are starting from. This usually includes your bank balance, credit cards, loans, and any money the business already owns or owes.

Your opening bank balance must match the real balance in your bank account on the day you start using the software. If it doesn’t, your reports will never fully line up when you go to reconcile.

4. Connect your bank accounts

Next, connect your business bank accounts and credit cards so transactions can flow into the software automatically.

Once this is connected, you can set up simple rules to handle repeating transactions, like rent, internet, or software subscriptions. This will help reduce manual work and keep your records up to date.

5. Set up payroll

If you have employees, you’ll need to add their details, pay rates, and benefits information. The software should also be connected to the ATO so payroll reports are sent automatically through Single Touch Payroll (STP).

This step is especially important to get right, as payroll errors can be time-consuming to fix later.

How to troubleshoot common problems

Even when you do everything right, you may find unexpected quirks in your system. Here are some common ones we see and how you can easily fix them.

My bank feed is not syncing

The first thing you should do is check whether the bank connection has expired or needs re-authorising. Trying to log back in and refreshing the feed usually resolves this. If this doesn’t work, reach out to the support team because the feed should work smoothly.

We keep getting duplicate transactions

If you see the same transaction twice, the first thing you can do is delete one copy. Next, check whether you’ve uploaded a bank file and connected a bank feed. If this is the case, turn off manual uploads once bank feeds are active. If not, check that you weren’t accidentally charged twice.

My GST looks wrong

The first thing to do is investigate the transaction, so click into it to get more details. From there, you may notice that your GST code was incorrect. For example, the system may have mixed up GST-free with standard GST.

Our opening balances don’t match

More often than not, this is because the dates aren’t matching up. Find the date you started from in the software and check your real bank balance on that day. If there are any numerical or date-based errors, edit them so they match.

My accountant can’t see everything in my system

This can happen when access settings aren’t correctly configured. Go to the settings in your system and find where to change your access settings. You’ll want to edit this so that your accountant has access to everything they need.

Ready to have more confidence in your numbers?

Bookkeeping software can organise your numbers, but it can’t tell you what they mean or how to act on them. That’s where Visory comes in.

At Visory, we help growing businesses make sense of their numbers. Our team works with you to select, set up, and optimise the right software for your business and then use that foundation to deliver clear financial insights you can act on.

This helps your business:

• Understand how revenue and expenses are trending month by month

• Set realistic yet ambitious goals and develop a plan to achieve them

• Make confident calls on when and how to invest, hire, or grow

• Bring insights into daily business conversations and decision-making

• Run board or leadership meetings with a clear, shared view of financial performance

If you’re ready to get expert financial insights that help you grow your business, book a meeting with one of our experts.

FAQs

How long does setup take?

For a small business, setup can be as fast as a single hour. However, for more complex businesses with payroll, multiple accounts, or historical data, you may need to clean up your data first, which can take a few days to get everything in place.

Can I switch accounting software mid-financial year?

Yes, and many businesses do. It’s easy to switch mid-year, as long as opening balances and GST are set up correctly from the changeover date.

What happens to my historical data if I switch?

You don’t lose it. In fact, it’s a great time to clean it up and bring it over to a better system. All of the options on this list know that businesses want to do this, and all have clear processes for migrating data from other software or spreadsheets.

What integrations matter most?

You’ll want integrations with software you already use and plan to keep using that touches your finances. This could include payroll software, POS or ecommerce platforms, payment gateways, expense management tools, inventory or stock systems, CRM tools, and more.

Do people like MYOB or Xero better?

This is the million-dollar question, and there isn’t one clear ‘better’ option. Depending on who you ask, you’ll get a different answer, as both platforms have avid fans.

However, MYOB was around earlier, and when Xero entered the market, it disrupted these older, legacy platforms like MYOB and QuickBooks. When we look at Capterra, Xero has a rating of 4.4 stars, and MYOB has 3.8. So, in the court of public opinion, Xero is the better platform.

Can I learn to use Xero by myself?

Yes, and this is partly why Xero has had so much success. The platform is made for sole traders and owners of small businesses who aren’t accounting professionals. You’ll notice it offers simple and clear dashboards and onboarding flows that help people go from Xero-novices to Xero-experts without a degree in finance.