He was falsely convicted of treason and executed following a purge within the army of the Holy Roman Empire that targeted officers associated with former Generalissimo Albrecht von Wallenstein.

Upon the death of his father Christoph and his relative Adam von Schaffgotsch, he inherited vast estates including Greiffenberg, Greiffenstein, Kynast, Giersdorf, Trachenberg-Prausnitz, Schmiedeberg as well as territories between the Riesengebirge mountain and the river Iser.

A year later, he was promoted to the rank of general by the new Imperial Generalissimo Albrecht von Wallenstein, participating in a short summer campaign that knocked Denmark out of the war.

He attended the coronation of Ferdinand III as king of Bohemia on 23 November 1627, during the accompanying tournament he received the title of Semperfrei [de] from the emperor.

Schaffgotsch took Thurn and general Jacob Duwall [sv] prisoners, displaying them in front of the garrisons of Liegnitz and Ohlau, which prompted their surrender.

Towards the end of 1633, the command of the Silesian front was transferred to Matthias Gallas and Rudolf von Colloredo, while Schaffgotsch was summoned to Pilsen reaching it on 4 January 1634.

His dislike of courtly life and the influence exerted by the church upon the emperor created an axis of undercover opposition that launched a smear campaign against him.

Numerous commanders signed the Reverse so as not to arouse suspicion, while at the same time a party centered around Ottavio Piccolomini began circulating an anonymous tract that summarized the army's grudges against Wallenstein.

Wallenstein's letters refuting the accusations against him remained unanswered, after realizing that the emperor was positioning troops in such a manner as to surround him he decided to flee to the Swedes, departing from his headquarters on 22 February.