Taxes etc

You need to speak with a qualified Gestoria  (Book-keeper/accountant) One that is a member or has a connection with the Colegio de Gestorias. In Spain anyone can set-up as a Gestoria. The Colegio members are regularly updated on the Spanish and EU tax regulations. When choosing a Gestoria don’t be afraid to ask for formal qualifications. 

Once you are a permanent resident you should be paying taxes in Spain. 

One option is to register the UK company (Ltd?) with the Spanish Social Security. The company then pays the Social Security payment to the Spanish system (about 500€ per month) You become a Spanish employee of the company. No sure how the income tax is paid on this arrangement.

Possibly you are paid gross and make a quarterly payment to the Spanish tax man. Maybe the company makes the deduction for tax and pays quarterly to the Spanish tax man. Either way your income tax is totalled up at the end of the year in your Spanish tax return (La Renta). 

Another option is to become a sub-contractor of the UK business. Autonomo in Spain invoicing the UK company monthly. The Social Security payment is currently 280€ per month and 50-70€ per month accountancy fees. Tax is collected quarterly at 20%. You will also need an EU VAT number. When you apply for an EU VAT number the VAT man likes to come for a visit ( Some sort of home office?). UK invoices become subject to the reverse charges rule. Ie. You don’t have to apply the VAT to the invoice. 

The advantages are you can claim business expenses against income. It all balances out in La Renta at the end of the year.

You won’t pay tax and social security in both countries but you do need a Gestoria to help decide which option brings the best benefit.