Before the most recent renovation, the church hall got new interior design for Christmas 1997. The interior was designed by architect Ilmar Kannelmäe. The walls were painted (partially) light blue and decorated with a pre-war style frieze with text “Come to me, all you who are weary and burdened, and I will give you rest”.
The stained glass cross was designed by Eeva-Aet Jänes. The new altar and the altar rails were inspired by pre-war style and by designs of Erik Pärn. Andreas Sester redesigned the pulpit by adding small details to it.
Estonian National Museum performed reconstruction works in its own section in 1987-88, the metal storage shelves date back to that period. The museum replaced the roof above the church hall in 1998 to set off the rent, but the new stone roof differed from the original roofing.
Spire was added to the church tower on the 10th of September 1999. The spire is made of copper sheet metal varnished to avoid darkening due to oxidation. The area in front of the church was paved with stones in autumn 2000. The Sports Museum gave up the building’s wing in 2001 and partial renovations were made.
Since 28th of July 2002, the church in cooperation with the Department of Social Welfare of Tartu City provides emergency social aid for those without any monthly income. The rooms in the basement of the church have been renovated for that purpose.
The part of the church formerly used by the Estonian National Museum was given back to the church on the 21st of September 2005. Finally, the building of St. Paul’s Church of Tartu was completely at the disposal of the church. Soon after that the renovations of the church were taken into consideration.
St. Paul’s church was fully renovated from 2005 to 2015. Renovation included construction of the rooms in the basement - crypt, columbarium and ancillary rooms. The wing and the church hall were fully renovated.
Re-consecration and formal opening of St. Paul’s Church of Tartu will take place on the 12th of September 2015. The program involves oratorio "Jonah’s Mission/Joonase lähetamine" by Rudolf Tobias.