[2] In June 1632, he was appointed by King Charles I as Secretary of State in succession to Lord Dorchester, his senior colleague being Sir John Coke, and he was knighted.

The first Earl of Portland, Francis, Lord Cottington, and Windebank formed an inner group in the council, and with their aid the king carried on various secret negotiations, especially with Spain.

[2] In December 1634 Windebank was appointed to discuss with the papal agent Gregorio Panzani the possibility of a union between the Anglican and Roman Churches, and expressed the opinion that the Puritan opposition might be crippled by sending their leaders to the war in the Netherlands.

[2] In July 1638 he urged the king to make war with the Scots, and in 1640, when trouble was breaking out in England, he sent an appeal from Queen Henrietta Maria to the pope for money and men.

In December the House learnt that he had signed letters of grace to recusant priests and Jesuits, and summoned him to answer the charge, but the king allowed him to escape to France.