I have SAYE on company option and it is taken from my monthly salary before tax deductions. So if you get £2000 gross per month you tax would be calculated after you take £100 for SAYE from £2000 =>taxable amount will £1900. The reason for this is that they assume you will actually carry on saving until money become tax free which is after 3 years. It would not make sense to deduct tax from it SAYE and after three years to give the tax back to you.

SAYE contributions will become taxable only if you decide to cancel your SAYE scheme. I know that because I cancelled my scheme twice to get a better option price when share price was falling. So I would get a cheque from a building society that looks after our company scheme for all the money I paid into the scheme e.g. 12 months x £100 = £1200

Following month the income tax for that £1200 would be deducted from my pay check.

SAYE is well worth it if you are close to a tax bracket and by using SAYE you can get back below it, and if you can afford to make the payments for the entire period it is well worthwhile.