You do have to pay back �1000 but if it's done by reducing your final salary payment the adjustment for tax/ NI will automatically reduce the amount you repay to approx. the �800 you received. The amount would be different if the tax regime had changed dramatically in the intervening period and you may win or lose a bit on NI depending on how the �1000 in one month affected your pay versus the various threshholds there are in the NI calc. If the repayment is made outside payroll then they should (at the time) quote you a lower figure to take account of the tax and NI you've paid.