Johann may have been raised in Rapperswil and even educated at the royal Habsburg court after the death of his father on 21 December 1337 on the occasion of a battle against Zürich-Toggenburg invaders at the Grynau Castle.

[4] Some, if not most of the refugees, were decades before their exile vassals of the Counts of Rapperswil, including the ancient councillors family Bilgeri those members lost four of their seats in the council of Zürich.

[5] On 21 September 1337 Graf Diethelm von Toggenburg moved from Zürich over the Obersee to the Grynau Castle at the confluence of the Linth river in the former Tuggenersee.

[7] On the basis of these facts, the feud was continued by Johann II in the late 1340s,[8] but there also was a short time alliance with the city of Zürich: On 28 September 1343 Count Johann II and his brothers Rudolf and Gotfried von Habsburg and the citizens of Rapperswil signed a document for an eternal confederacy with the city council and the citizens of Zürich.

An attempted coup by Brun's opposition, known as äusseres Zürich, in the city of Zürich was forcefully put down after intensively forced street fights around the Münsterhof plaza on 23/24 February 1350: Count Johann II, now the opposition's leader, was arrested for two years, and the town walls of Rapperswil, its castle and Altendorf castle were destroyed by Brun.

[13] The division of the estate between the Counts Rudolf, Gotfrid and Johan von Habsburg was regulated in a document on 1 July 1354: Johan received the town of Rapperswil with all accessories and what is on this side of Zürichsee; 110 pound annual interest on the tax from Glarus that was pledged for 400 silver marks to the Dukes of Austria; the right to initiate all pledged assets at the right bank of the lake and the Greifenberg castle (present Bäretswil) and the valley of Fischental (Tösstal).

[15] All rights related to lands in the Höfe district including the settlements at Bäch, Pfäffikon and Wollerau were sold by Count Goetfrid von Habsburg-Rapperswil on 19 May 1358.

With his brother Rudolf IV, Johann was mentioned around 1354 and 1364 in Italy as a condottiere (military leader) for the Italian city republic of Florence.