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Tax and paying Living Allowance

Processing payroll for the first time, new starter entitled to Living Allowance on top of Salary

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Hello all,

I have recently took on my first role as an accountant/bookkeeper for a shipping company, The reason for my employment is because there is a huge backlog of transactions/accounts which needs to be sifted through (I will ask lots of questions another time). The basis for my question is that the bookkeeper who has handled the accounts for a long time has gotten behind, and now has been taken ill. Which means I am being entrusted with payroll for the first time. Usually, salaries are set up through the bank and PAYE is calcualted on the HMRC Basic PAYE tools software, but I have had a new starter come in whom is also entitled to Living Allowance. I have managed to use the UK Salary Calculator to work out what his monthly pay would be, but can someone please advise on how Living Allowance will be paid? Do I need to deduct anything? Should this be kept completely seperate to the salary? Any help would be greatly appreciated. Thanks!