Queen Gunilla is acknowledged to have acted as the political adviser to John III and to have influenced his religious policies in favour of Protestantism.

About half a year after the death of his first queen in 1583, John III chose Gunilla to be his next consort, after first having considered Sigrid Brahe.

Asked why he did not marry a member of a princely house, John III openly stated that he wished to have a beautiful consort and that portraits of foreign princess were not to be trusted.

[2] Similar to the mother and stepmother of John III, Margareta Leijonhufvud and Katarina Stenbock, Gunilla was already engaged when the King decided to marry her.

Because of the controversy around the marriage, John III was eager to make the occasion as impressive as possible, and arranged many celebrations of the event, such as a tournament, where Queen Gunilla officiated by handing out the prizes to the winners.

After his marriage to Gunilla, John III's efforts to introduce the Counter Reformation in Sweden effectively ceased, and she is known to have acted in favour of persecuted anti-liturgical priests on several occasions.

[3] Gunilla accompanied John III to the council in Reval in Swedish Estonia in 1589, where the monarch came into conflict with the councillors of the noble parliamentary estate.

Her brother-in-law Duke Charles, the future King Charles IX, portrayed her in a very bad light in this regard and accused her of using her influence over the king to promote her family with a rhyme in his chronicle: In 1590, John III left instructions for Queen Gunilla to serve as regent, should his son with her succeed to the throne while being still a minor.

When the son of Charles XI, King Gustav II Adolf of Sweden, wished to marry another member of the nobility, Ebba Brahe, in the 1610s, his mother Christina of Holstein-Gottorp opposed the match with a reference to the marriage between John III and Gunilla Bielke as a bad example, and eventually prevented it.

Duke Charles, who had been received constant reports of the king's health during his illness, claimed that Gunilla had concealed the death of the late monarch for days while stealing from the Royal Castle's belongings.