Automated payroll

The features of inniAccounts’ payroll are designed to take the administrative pain out of running your company payroll.

Once you’ve set up your company payroll by entering the salary payments you’ll make to directors and employees, each time pay day arrives inniAccounts will automatically calculate and issue your payslips. In this guide you’ll discover how to control this process.

A business normally pays its directors and any employees a salary each month. Before an employer can pay salaries they must register with HMRC. The business can then run payroll and submit information to HMRC each payday using an interface called Real Time Information (RTI).

Timely and accurate RTI submissions are critical to avoid penalties being automatically issued by HMRC. You do not need to worry too much about RTI, your automated payroll will manage the interface automatically for you.

Setting up and managing payroll

Your inniAccounts Account Manager will configure the payroll for your company directors and employees. Once everything is in place and connected to HMRC via RTI, they’ll be in contact to discuss with you. It will then be time to set up your payroll for the first time.

Payroll is a repetitive cycle, in other words you will carry out the same procedures each month. It is good practice to document your payroll procedures as each company will have specific processes for example around signoff. The basics of using InniAccounts remain the same however, and are as follows:

Your first step, carried out before each payday is to log into inniAccounts and preview your payslips.

1. Previewing your first payslip

To preview your company’s payslips first click on Withdrawals and then select Payroll. You’ll see a message about your next payroll date. Click on the button Preview payslip to preview your upcoming payslips.

It is here that you can check and if necessary, edit your payments.


2. Setting or amending salaries

The salary item can be split into three components, basic salary, bonus and overtime. All three types of pay are treated the same for tax purposes, but the split is necessary for your internal reporting and also to assist your employee in understanding what he or she has been paid.

Choosing a salary for directors

A director or owner with appropriate permissions may wish to consider their options with regard to tax efficiency when deciding how much to pay themselves. For further reading, click here.


An employee’s salary is typically a regular, repeatable payment. You can edit an employee’s salary by clicking on the pencil next to salary, where you’ll be presented with three options:

  • Regular salary – Here you can enter their annual salary and inniAccounts will automatically calculate how much to pay them on each payslip depending upon the number of paydays you have. Note: when you change an employee’s salary it will update all future payslips.
  • Temporarily change their salary – This option is useful if you need to make a temporary adjustment to pay but do not wish to change the stated annual salary. For example, you may wish to suspend payment for a period of time or indeed indefinitely. If you need to do this, the system will provide you with an option to select to apply the change as a one-off (i.e. apply it only to the next payslip), apply it to a specified number of payslips, or apply it until you choose to remove the change (e.g. to suspend salary payments indefinitely).
  • You can also choose to skip their salary payment altogether

Bonus and overtime

You can choose to pay your employees a bonus or overtime at any time by clicking on the pencil icon. As with salaries, you have the option as to how long you wish to make the payment for.

For example, it may be a one off annual bonus or in contrast, an overtime arrangement where you have agreed to extra pay for a period of weeks or months.

3. Reimbursing mileage and expenses

You can also choose to repay personally incurred expenses to your employees that have been entered in the Quick Entry area as well as journeys recorded in the mileage log.

To do so, simply click on the relevant pencil. You must choose whether you wish to automatically repay all expenses and mileage to a given employee, or to manually select those items you wish to repay.


It’s also possible to use a combination of the two methods. In the above screenshot you can see that the Carpark charges will be repaid to this employee. It is possible to choose an alternative employee to repay the other expenses.

If you set an employee to be repaid either expenses or mileage automatically, the repayments will be recalculated on the date that the payslips are created. This means that the preview of the payslips during this process may differ from the payslips that are actually issued. This would occur for example, if you enter additional expenses into inniAccounts after previewing the payslips.

The creation and issuance of payslips

A week before your pay date we will send you an email to remind you to check your payslips. You should check salary payments and reimbursement of mileage and expenses for each individual on your payroll.

RTI submission rules

It is worth reiterating the importance of checking your payroll data as once payslips have been submitted to HMRC, they cannot be edited, deleted or amended. If you do find an error later you will need to correct it on a future payslip.

Once pay day arrives, the application will automatically create payslips for your employees based on the information previously provided. These payslips will then be sent electronically to HMRC (via RTI).

When your payslips have been confimed as accepted by HMRC you will receive an acknowledgement email from them. We will also send you an email detailing the payments you need to make to your employees.

Making payments to employees

Once your payslips have been issued, you must then pay your employees. The email from us referenced in the section above details the payments that you need to make. Alternatively, you can also see a list of payments on your company’s dashboard and also in the bookkeeping area.

You need to transfer the net amount referenced in the payment record from your business bank account to the personal bank account of the individual. Remember to give each employee a copy of their payslip.

Once you’ve paid your employees, mark the transaction as paid during your normal bookkeeping activities.

Exporting payslips

In the event of queries you are able to email payslips to your employees or export copies in PDF format by clicking to view your payslips.

Making Tax and National Insurance payments to HMRC

You need to make regular payments to HMRC for:

  • Income tax deducted
  • National Insurance deducted
  • Student Loan repayments

This can be either a monthly or quarterly process depending upon your organization but in both cases we will send you an email when the payment is due.

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inniAccounts Ltd
1 Derwent Business Centre
Clarke Street

Registered in England


0800 033 7827

Calling from overseas
+441332 460 010

Contact us

Contact inniAccounts



0800 033 7827

Calling from overseas

+441332 460 010

Head Office

1 Derwent Business Centre
Clarke Street