He was in the beginning of the troubles very hearty and strong for the Parliament, and manifested great personal courage, honour, and military as well as civil abilities, as appears by his actions and letters, whilst he was in the service of the Parliament. In whose favour and esteem he was so high that they voted him to be general of the horse under the Earl of Essex, and afterwards to be an Earl. But having taken a disgust of the Parliament's declining of a personal treaty with the King, and being jealous that monarchy, and consequently degrees and titles and honour, were in danger to be wholly abolished, he was too forward in countenancing and assisting the late tumults in the city, when the members of Parliament were driven away from Westminster to the army. Upon the return of the members he was, with other lords, impeached of high treason for that action, and rather than appear and stand a trial for it he left his country and revolted to the King, and was now with the Prince in his navy, for which the Commons voted his estates to be secured. Rupert was at the time carrying on privateering hostilities against the Parliament with such energy that, as was said, a packet-boat could hardly sail from Dover without being pillaged, unless it had a convoy. Willoughby accepted a commission, and became admiral of the Prince's fleet, and in the month of August, 1648, while in the Downs, was fortunate enough to intercept and capture a vessel returning from Guiana with a cargo of merchandise and £20,000 in gold. The year following the execution of the King he went out to Barbadoes, established himself as governor, and proclaimed Charles II. king. On hearing of this exploit, Cromwell's government despatched Sir George Ascue with a fleet to effect the reduction of the place; after several ineffectual attempts to obtain submission he landed a force and stormed the fortress, when Lord Willoughby, fearing a revolt of the garrison, yielded on honourable terms, which included protection for the enjoyment of his estates. He then returned to England, but the Republicans, being doubtful of his loyalty to the Commonwealth, caused him to be committed to the Tower (June, 1655) on the charge of high treason. He must have remained in confinement for a considerable period, for two years later we find him petitioning Cromwell for permission to go into the country to despatch some necessary business in relation to his estates, and promising to return to prison--a request that was complied with. He subsequently obtained his release, and, after the death of Cromwell, appears to have co-operated with Monk in effecting the dissolution of the Commonwealth and the recall of the exiled Stuarts.