Can My Accountant Set Up My Bookkeeping Software for Me?

Introduction

If you are starting a new business or switching from manual records to digital bookkeeping, you might wonder whether your accountant can set up your accounting software for you. The short answer is yes. Most modern accountants not only recommend bookkeeping software but can also set it up, customise it, and train you to use it effectively.

Bookkeeping software is now a key part of running any successful business. It helps you track income and expenses, issue invoices, manage VAT, and prepare reports for tax and decision-making. However, setting it up correctly from the start is crucial. In this article, we explain how accountants can help, what the process involves, and why getting professional support saves time, money, and frustration.

Why Bookkeeping Software Matters

Since the introduction of Making Tax Digital (MTD), HMRC requires many businesses to keep digital records and file returns using approved software. Even if you are not yet mandated to do so, accounting software makes financial management far easier and more accurate. It reduces paperwork, minimises errors, and gives real-time insights into your cash flow and profitability.

Choosing the right system and configuring it properly ensures your accounts run smoothly from day one. This is where your accountant’s expertise becomes invaluable.

How an Accountant Can Help Set Up Your Software

A professional accountant understands both your business needs and the software’s technical setup. They can tailor the system to fit your structure, ensuring every transaction is categorised correctly and complies with tax requirements.

Here is how your accountant typically helps during setup:

1. Choosing the right software
   Accountants work with platforms such as Xero, QuickBooks, FreeAgent, and Sage. They can recommend which one best suits your business size, industry, and reporting needs.

2. Initial installation and configuration
   Your accountant can create your company file, input your opening balances, and set up the correct chart of accounts so that income and expenses are categorised accurately.

3. Bank feed integration
   They can link your bank accounts securely to automate transaction imports, reducing manual entry and improving accuracy.

4. VAT and payroll setup
   If you are VAT registered, your accountant ensures your VAT settings are correct and that MTD filing is enabled. They can also configure payroll if you pay employees or directors.

5. Customising invoices and templates
   Accountants can help you create branded invoice templates, payment reminders, and quotes that look professional and integrate seamlessly with your system.

6. Testing and training
   Once everything is ready, your accountant can test the system with sample entries and train you or your staff to use it confidently.

By managing this process, your accountant ensures your bookkeeping software is fully compliant and ready to go from day one.

Common Mistakes When Setting Up Software Yourself

Many business owners attempt to set up their own bookkeeping systems but run into problems later. Common issues include:

• Selecting the wrong VAT settings or accounting method (cash or accrual basis)

• Duplicating transactions due to incorrect bank feed setup

• Misclassifying income or expenses

• Forgetting to carry over opening balances

• Using inconsistent account categories that confuse reporting

These mistakes can cause errors in your financial records, which might affect VAT returns, tax submissions, or management accounts. Having your accountant set up the system avoids these pitfalls entirely.

Benefits of Having Your Accountant Handle Setup

Working with your accountant on software setup offers several clear advantages:

• Accuracy: Everything is configured to match accounting standards and HMRC requirements.

• Time savings: You can start using the system straight away without struggling through technical details.

• Consistency: Your accountant ensures the data structure aligns with how they prepare your accounts and tax returns.

• Ongoing support: If you ever have questions or issues, your accountant already understands your setup and can resolve them quickly.

• Better decision-making: Properly structured data leads to reliable reports and better business insights.

Integration with Other Systems

Many businesses use other tools alongside their bookkeeping software, such as e-commerce platforms, CRM systems, or expense apps. Your accountant can integrate these with your accounting system so that data flows automatically. For example, they might connect Shopify or PayPal to Xero or link your mileage tracker app to QuickBooks.

These integrations save hours of data entry and reduce the risk of missing or duplicate transactions.

Ongoing Bookkeeping Support

Once your system is live, your accountant can also manage or oversee your bookkeeping on an ongoing basis. This could include reconciling bank transactions, posting invoices, processing payroll, and preparing VAT returns. Some businesses prefer to handle daily input themselves while letting their accountant review and reconcile monthly.

This hybrid approach keeps you in control while ensuring everything remains accurate and compliant.

What You Need to Provide

To help your accountant set up your bookkeeping software effectively, you will usually need to provide:

• Access to your business bank accounts or statements

• Copies of recent invoices and receipts

• Information on any existing accounting system or spreadsheets

• Details of VAT registration, payroll, and company structure

• A list of suppliers and customers if you want these imported

Providing this information in advance ensures a smooth and accurate setup.

Example Scenario

Imagine a small construction company that has kept its accounts in Excel for years. As business grows, the owner wants real-time visibility of cash flow and VAT liabilities. Their accountant recommends Xero, sets it up with the correct chart of accounts, integrates the business bank feed, and imports past transactions. They also customise the invoice template and set up MTD VAT submissions.

Within a few days, the system is live. The owner can now raise invoices from their phone, track payments automatically, and view profit reports at a glance. The accountant reviews the data monthly to keep everything up to date.

Training and Guidance

A good accountant will not only set up the software but also teach you how to use it properly. They can explain how to create invoices, upload receipts, reconcile payments, and generate reports. This guidance helps you stay confident and independent while knowing expert help is always available.

Cost of Setup Services

The cost of having your accountant set up bookkeeping software varies depending on the system and complexity of your accounts. For a small business, setup might cost between £150 and £500. Larger or more complex setups with integrations and multi-user access can cost more.

Although this is an additional expense, it often saves far more in the long run by preventing errors and ensuring compliance. Many accountants include setup as part of a wider bookkeeping or accountancy package.

Conclusion

Yes, your accountant can absolutely set up your bookkeeping software for you. They can recommend the right platform, configure it correctly, integrate your bank feeds, and train you to use it confidently. Getting professional help ensures accuracy, compliance, and efficiency from day one.

Whether you are starting a new business or upgrading your systems, letting your accountant handle the setup gives you peace of mind and saves valuable time. With everything running smoothly, you can focus on what really matters — growing your business.