He received the degree of Doctor of Medicine, and in 1575 was appointed court physician to the Margrave Karl II of Baden-Durlach, who frequently sought his advice in political and theological matters.
He went to Freiburg, became a priest in 1591, then vicar-general of Constance until 1594; after this he was an imperial councillor, cathedral provost of Breslau, Apostolic prothonotary, and in 1601 confessor to the Emperor Rudolph II.
Pistorius published a detailed account of the conversion of Margrave James III: "Jakobs Marggrafen zu Baden ... christliche, erhebliche und wolfundirte Motifen" (Cologne, 1591).
Pistorius also busied himself with cabalistic studies, and published "Artis cabbalisticæ, h. e. reconditæ theologiæ et philosophiæ scriptorum tomus unus" (Basle, 1587).
As court historiographer to the Margrave of Baden, he investigated the genealogy of the princely House of Zähringen; he also issued two works on historical sources: "Polonicæ historiæ corpus, i. e. Polonicarum rerum latini veteres et recentiores scriptores quotquot exstant" (Basle, 1582), and "Rerum Germanicarum veteres jam primum publicati scriptores aliquot insignes medii ævi ad Carolum V" (Frankfort, 1583–1607).