Since 1st April 2016, those purchasing a second home that does not replace a previous main residence have been liable for an additional 3% stamp duty on the purchase. Married couples and civil partners are treated as one unit for this purpose.
If the couple jointly owning a home are separating their treatment as one unit could cause problems. They will only be treated separately and not incur the additional levy if they are legally separated under a court order or a deed of separation or are living separately in circumstances that are likely to become permanent. The additional levy will be payable on a second home purchase in all other circumstances, but, if the former family home is sold or transferred to the other partner within 36 months, HMRC will provide a full refund.