Despite pressure from the KGB, Lithuanians organized folklore and ethnographic ensembles, lit the bonfires on Rasa and candles on Vėlinės (All Saints' Day)—symbols important to the cultural vitality of the nation.

With the beginning of Sąjūdis (the Reform Movement of Lithuania), Trinkūnas was able to return to the university and worked as an assistant at the Ethics division of the Institute of Philosophy and Sociology.

From 1994 he worked as a researcher at the Ethics and Ethno-Sociology division of the Institute of Philosophy and Sociology; he lectured on ethnic culture at Vilnius Pedagogical University, participated in numerous international conferences and events related to old pagan faiths, authored many articles in both the Lithuanian and foreign presses and penned several books.

He was a member of the ritual folklore ensemble Kūlgrinda, Etninės kultūros draugija (Ethnic Culture Society), Tautos namai (Home of the Nation), Mažosios Lietuvos reikalų taryba (Board of the Affairs of Lithuania Minor), Prūsa club and other organisations.

As Head of the Ethnic Culture division, Trinkūnas demanded that a special Jonas Basanavičius Award be founded, which would stimulate folklore research and activities.

In 2002, Trinkūnas was ordained as Krivis (High Priest) of Romuva and was given the name Jaunius (from jaunas meaning “young”), symbolising the rebirth of the ancestors' faith.