After the election of 1963 Bakker was appointed as State Secretary for Economic Affairs in the Cabinet Marijnen, taking office on 3 September 1963.

The Cabinet Cals fell just one year later on 14 October 1966 and continued to serve in a demissionary capacity until it was replaced by the caretaker Cabinet Zijlstra with Bakker appointed as Minister of Economic Affairs, taking office on 22 November 1966.

In January 1971 Bakker was nominated as CEO and chairman of the board of directors of Ago Insurance; he resigned as a member of the House of Representatives the same day he became CEO and chairman of Ago Insurance serving from 15 February 1972 until 1 January 1983.

Bakker also became active in the private sector and public sector and occupied numerous seats as a corporate director and nonprofit director on several boards of directors and supervisory boards (ING Group, Zilveren Kruis) and served on several state commissions and councils on behalf of the government (Staatsbosbeheer, Netherlands Cadastre Agency, Sociale Verzekeringsbank and Public Pension Funds PFZW) and as a diplomat and lobbyist for several economic delegations on behalf of the government.

Bakker later served as chairman of the supervisory board of the DSM Company from 1 May 1984 until 1 July 1988.