Stamp Duty at Higher Rate Confusion for Landlords

Please could anyone help me as I hate paying over tax to this horrible government in error and I am sure I have made a mistake here through a lack of knowledge about stamp duty.

In August 2017 I bought a large property as my main residence (property A) during that time I ran into financial difficulty and was forced to sell and had to accept a low offer on this my main residence property, the purchaser also part exchanged his lower priced terraced property as part of the deal.

The property that I had to accept as the part exchange (property B) was in a rough area that I did not want to live in and also not in the catchment for the correct schools. Money was really tight and the property would have been difficult to sell so I decided to rent it out.

What this meant was that I had sold my larger main residence and split the proceeds into a lower priced property that I rented out and also had some cash in the bank.

I then decided to rent a house for myself for around 12 months to get a grip on my finances and look for a cheaper property to buy in the area I wanted to live. eventually I bought a much smaller cheaper property (property C) in the area I liked with good schools in the same town I was renting.

Over the next few years I worked hard and improved this property so its value has increased and I am now in the process of part exchanging this property which is my main residence to a larger property in the same town (property D) During all this time I still have the rental (property B)
that was part exchanged against my original main residence.

Sorry about this but now I finally get to ask my question and problem regards stamp duty which I am sure I have not done correctly but I need some advise as I cannot work it out.

On buying property C my main residence I was charged the higher rate stamp duty as I owned 2 properties - this property as my main residence and the forced rental.

Now I am selling Property C and buying property D which will also be my main residence but I am being asked to pay the higher rate stamp duty again as a 2 property owner.

So in the space of around 3/4 years I have paid the higher rate of stamp duty of 2 houses that have been my main residences because it is seen that I have 2 properties because of the forced rental property.

Can anyone clear this up for me as from what I am reading I feel I have done something wrong here and should not have paid the higher rate as these are my main residences even though I have a second rental property?

Many thanks Emma

I’m no expert in SDLT, but from my limited knowledge of the regulations, you should not be charged the extra 3% for replacing your main home even if you own other properties. How long did you live in property C? Is it being treated as a development property for tax purposes? I’m also wondering whether the part exchange route means you are deemed to be buying D before selling C?

I think it would be worth your while getting advice from a tax specialist, who might be able to put a case to HMRC for a refund of the 3%.

Many thanks for the Reply David, yes i think I need a tax expert to look at this.

Stamp Duty Land Tax: Residential property rates - GOV.UK

"If you’re replacing your main residence

You will not pay the extra 3% SDLT if the property you’re buying is replacing your main residence and that has already been sold.

If you have not sold your main residence on the day you complete your new purchase you’ll have to pay higher rates. This is because you own 2 properties.

You can apply for a refund if you sell your previous main home within 36 months."