There is a common misconception that the mortgage that you can get is 4.5x your salary. This leads some to believe that salary exchange will impact the amount you can get for a mortgage. In reality, there are two things that stop this from being the case:
The way your mortgage is actually calculated
The concept of notional salary
The way your mortgage is actually calculated
Mortgages are actually calculated using a range of different data sources that ultimately figure out how much you can afford to pay and therefore the likelihood you have of paying back the money you have been lent.
As you are aware, you pay your mortgage after you pay tax. In salary exchange, your after-tax income is going to be the same (if you opted for boosted pension contributions) or higher (if you opted for boosted take-home pay). Therefore your ability to afford a mortgage has either stayed the same or increased.
The concept of notional salary
Notional or 'reference' salary refers to your salary before any exchanges are made, as HMRC describe it: "[notional salary is] a useful summary of the value of the remuneration package as a whole which is made up of cash and benefits".
According to HMRC, employers and employees can use notional or reference salary in a number of situations including to provide information about earnings to a mortgage lender.
Special cases
The Help to Buy Scheme
The Help to Buy Scheme is based upon the purchase price of the property that is being bought and not on your earnings. You can borrow up to 20% of the purchase price of the property (40% in London) providing that the overall amount being lent is approved by the mortgage lender.
The way your mortgage is calculated is the same as in the above section, i.e. there is no detrimental impact of salary exchange on the mortgage available to you under the Help to Buy Scheme.