Within weeks, however, the fortunes of war turned and the troops of the ruling king and the Hungarian lords loyal to him recaptured the lost Transdanubian territories. Keszthely was forced to surrender by the troops of Török István of Enying, the Chiefl Captain of Pápa castle, and to return to the allegiance of the crowned Habsburg king.

The new captain of Keszthely was Bakacs Sándor (Bakács, Bakach) of Szentgyörgyvölgy, who, in addition to his office, was also the owner of most of the estates around Keszthely castle through his wife Pethő Kata of Gersei and had applied for the captaincy several times before. However, he could not even take up his new post – as he was involved in the preparation of the action against the fortress of Kiskomárom, which remained on Bocskai’s side, and the Ottoman auxiliaries stationed there – while the war situation suddenly turned again.

The troops of the Sanjak Bey of Koppány castle stationed near Kiskomárom suddenly launched an attack and together with the Hungarian forces of Némethy Gergely, with their mere presence, forced several smaller Borderland forts to Bocskai’s side again, including Keszthely on 20 August 1605 – for the second time. The smaller part of the garrison, led by Fejér Mihály, left the garrison and sided with the lawful captain, Bakacs Sándor, while the larger part of the garrison and the hundred infantry and fifty cavalrymen, who were led to Keszthely on the proposal of Nádasdy István, remained (at least in principle) loyal to Bocskai until the Peace of Vienna in June 1606, and were mainly engaged in raids, robbery and pillaging in the surrounding area and Austrian territories.

After the Peace of Vienna in June 1606, however, a strange situation arose in Keszthely. According to the terms of the peace, the fortresses and goods that had fallen into the hands of the rebels had to be returned to the crown within a short time. However, the guards of Keszthely resisted the surrender and refused to let Captain Bakacs Sándor in. For this reason, at the end of May 1606, Archduke Matthias was forced to order that Captain Bakacs Sándor and the new ‘Keszthely’ garrison at his disposal be temporarily stationed at Szigliget Castle and to order the resisting Keszthely soldiers to obey.

Against all the odds, the Keszthely guards did not accept Bakacs’ appointment, and supported the appointment of Gersei Pethő István, a local landowner, as captain. Pethő’s request was also supported by Zrínyi VI Zrínyi and Széchy Tamás of Rimaszécs, who had been the chief captain of Transdanubia since 1609, while Bakacs Sándor had been appointed in 1605 by Ruprecht von Eggenberg, the chief captain of Győr, and his successor Hans Breuner, as well as Battyhány II Ferenc, the chief captain of Körmend and Transdanubia also supported him. However, his appointment still lacked Imperial approval. The Emperor finally gave his formal permission for Bakacs’ appointment in October 1608. In the same year, the Diet also enacted the provisions of the Peace of Vienna.

Despite all this, Bakacs Sándor of Szentgyörgyvölgy, the legal captain of Keszthely, was still unable to take up his post and was forced to serve as Keszthely’s captain in Szigliget Castle, at the head of the ‘Keszthely’ garrison at his disposal. The motives of the resisters were primarily existential. They were strongly afraid of their old-new captain, whom they opposed and sided with Bocskai in August 1605, and especially of being let go after filling his position, since he already had a new ‘Keszthely’ garrison at Szigliget. In addition, they resented the fact that they had not received their pay since their transfer in 1605, and rightly so.

The ruler wanted to resolve the aggravated situation by peaceful means, so he offered a thousand Rhaetian Forints – partly in cash, partly in the broadcloth – to the defiant soldiers of Keszthely, who refused the offer. Then, the Court Military Council preferred a violent solution. They ordered General Hans Breuner, the chief captain of Győr, to immediately install Bakacs Sándor of Szentgyörgyvölgy as captain, using armed force if necessary. In July 1609, troops were sent from Győr, Pápa, and Veszprém to Keszthely to underline this, but they refused to let them in.

This is how the repetition of the 1600 Pope’s mercenary rebellion and recapture of the castle – that is, the recapture of a Hungarian stronghold from the rebels by the royal troops by armed force, by siege – took place. The siege of Keszthely was between late July and early August 1609, and the fierce fighting was marked by the fact that, although it lasted only a few days, nine of the royal troops besieging the castle lost their lives and there were several casualties among the defenders. Finally, the ‘fire tools’ thrown into the castle forced the rebels to surrender, and they gave up further fighting and capitulated with impunity.

The agreement seems to have been kept, as neither Gersei Pethő István nor the rebel soldiers were prosecuted, and only two Hajdú soldiers were imprisoned. The acrimonious relationship between Pethő and Bakacs was resolved in the autumn when the parties came to an understanding and Bakacs appointed his rival as  Vice-Captain.

Although the Ottomans laid a major siege against it in 1650, they could never take the city and it always remained under the rule of Royal Hungary. Later the castle lost its military importance so the Habsburgs had it destroyed in the 18th century.