This will depend on your circumstances.
If a dispute relates to a tax avoidance scheme, HMRC can issue an accelerated payment notice (APN) that requires you to pay the disputed tax amount within 90 days.
If you have not received an APN, there is still an option to pay the disputed tax to HMRC upfront. Payment of the tax will stop additional late payment interest accruing. Given that some tax disputes can be lengthy, this can be an attractive option as HMRC is obliged to return undisputed payments. If a tax dispute can be resolved quickly, some people and businesses prefer to make the payment once an agreement has been achieved.
If you are concerned about when to pay the disputed tax amount, you may wish to speak to a tax expert for further guidance.