In 1600 and 1601 Zamoyski took part in the war against Sweden commanding the Commonwealth forces in Livonia (Inflanty). At the same time he was a vocal opponent of that war on the political scene. In 1600 he recaptured several strongholds from the Swedes and a year later captured Wolmar on 19 December 1601 Fellin on 16 May 1602, and Bialy Kamien on 30 September 1602. The rigours of the campaign, however, placed a strain on his health, and he resigned the command.