The Office is in a prominent location east of Berlin's central railway station at Kapelle-Ufer on the Spree river, opposite the Federal Chancellery and the Reichstag. Previously working in three different buildings, the Berlin-based staff of the Ministry – around 350 – moved to the new central building in autumn 2014. The Institute for Federal Real Estate (BImA) has rented the part of the premises and rooms not needed by the Ministry. In August 2011, the BImA awarded the contract for construction of the new building to a consortium led by the firms BAM Deutschland AG and Amber GmbH.

It is the first civil federal building which was planned and constructed and is being financed and operated as a public-private partnership (PPP) of the government and the private sector. The tendering procedure for the new BMBF building showed that a PPP can optimize both quality and costs. This pioneering effort produced a building of high architectural quality befitting its prominent address.

Its technical installations are exemplary in meeting the sustainability and energy efficiency requirements laid down in the Federal Government's energy and climate protection policy. The building was rated in the "Gold" category of the Assessment System for Sustainable Building (BNB). A smart grid linking the individual components of the energy supply system including a gas-powered fuel cell, a combined heat and power station as well as façade and rooptop solar panels enables low-emission autoproduction.

The building was planned by the renowned architects Heinle, Wischer und Partner, Berlin. After the Berlin House of Representatives approved the development plan, the Senate Department for Urban Development issued the partial building permit for excavation and pit sheeting work. This was the starting signal for construction of the new Ministry building. By 27 October 2014, the Berlin staff of the BMBF had moved into their new office. The Ministry's headquarters remain in Bonn where 75 per cent of the BMBF's staff are employed.