When he came of age, he left the administration of the County of Burgundy (Franche-Comté) to King Theobald I of Navarre to engage in the struggle around his Bavarian possessions against the ducal House of Wittelsbach.
He lost his position as a vogt of Tegernsee Abbey as well as the ancestral seat in Andechs, but retained the possession of Innsbruck, which he elevated to a town in 1239 and put under the administration of his father-in-law Count Albert IV of Tyrol.
In the fierce controversy between Emperor Frederick II and Pope Innocent IV, he sided with his feudal lord, the bishop of Bamberg, which earned him an Imperial ban and a large-scale loss of his possessions.
Childless, he was succeeded in Burgundy by his sister Adelaide and her husband Count Hugh of Chalon, while the Duchy of Merania expired.
With the death of Otto's uncle Patriarch Berthold of Aquileia in 1251, the House of Andechs became extinct.