At the beginning of the Thirty Years' War John Frederick and his prince-bishoprics of Bremen and Lübeck maintained neutrality, as did most of the territories in the Lower Saxon Circle.

After 1613 King Christian IV of Denmark and Norway, being in personal union Duke of Holstein within the Holy Roman Empire, turned his attention to gain grounds by acquiring the prince-bishoprics of Bremen, Verden, Minden and Halberstadt.

In November 1619 Christian IV of Denmark, Duke of Holstein stationed Danish troops in the Bremian city of Stade, officially on behalf of his son the provided to be Administrator successor, suppressing an unrest of its burghers.

John Frederick and the Bremian Estates met in a Diet and declared for their territory their loyalty to Ferdinand II, Holy Roman Emperor, and their neutrality in the conflict.

With Danish troops within his territory and Christian the Younger's request John Frederick tried desperately to keep his Prince-Archbishopric out of the war, being in complete agreement with the Estates and the city of Bremen.

The population suffered from billeting and alimenting Baden-Durlachian, Danish, Halberstadtian, Leaguist, and Palatine troops, whose marching through the John Frederick had to tolerate in order to prevent entering into armed conflict.

In 1623 the Republic of the Seven United Netherlands, diplomatically supported by James I, King of England, the brother-in-law of Christian IV of Denmark, started a new anti-Habsburg campaign.

So in 1628 he consented that the Lutheran convent in the former Premonstratensian Our Lady's Friary [de] in Stade – under Leaguist occupation – was restituted to Catholic rite and manned with foreign monks, if the Chapter would also agree.

The Leaguist takeover enabled Ferdinand II, Holy Roman Emperor, to implement the Edict of Restitution, decreed March 6, 1629, within the Prince-Archbishopric of Bremen.

Under the threat of the Edict of Restitution John Frederick consented to Canonical Visitations of the remaining monasteries, those clinging to Roman Catholic rite and those converted to voluntary Lutheran convents alike.

Within the scope of the visitations by the end of the year 1629 the Roman Catholic visitors issued an ultimatum to the Lutheran conventuals to convert to Catholicism or to leave the convents.

No conversion had been recorded, so at different dates between before Christmas 1629 and April 1631 all Lutheran conventuals had been thrown out from the nunneries, with the estates of Himmelpforten and Neuenwalde then being bestowed to the Jesuits, in order to finance them and their missioning in the course of the Counter-Reformation in the Prince-Archbishopric.

So Ferdinand II himself dismissed him by way of using the Edict of Restitution, in favour of his youngest son, the Roman Catholic Leopold Wilhelm, Archduke of Austria, already prince-bishop of Halberstadt (1628-1648), Passau (1625-1662) and Strasbourg (1626-1662).

For the war being John Frederick accepted the supreme command of Gustavus II Adolphus, who promised to restitute the Prince-Archbishopric to its former Administrator.

In October an Army, newly recruited by John Frederick, started to reconquer the Prince-Archbishopric and – supported by Swedish troops – to capture the neighboured Prince-Bishopric of Verden, de facto dismissing Verden's Catholic Prince-Bishop Franz Wilhelm, Count of Wartenberg, (ruled 1630–1632) and causing the flight of the Catholic clergy wherever they arrived.

In the same year Pope Urban VIII provided the Catholic coadjutor Leopold Wilhelm, Archduke of Austria, imposed in 1629 by his father Ferdinand II, with the Archdiocese of Bremen, but due to its persisting occupation by the Swedes he never gained de facto pastoral influence let alone the power as prince-archbishop.