Museum Boijmans Van Beuningen was one out of the four hundred Dutch museums which participated in the research project Museum Acquisitions 1940-1948 of the Netherlands Museums Association (NMV) in 1998-1999. The final report of this project was published in December 1999 by the NMV: E. Muller, Rapport Museale Verwervingen 1940-1948 (Report Museum Acquisitions 1940-1948) (in Dutch, with English summary). The municipality of Rotterdam has commissioned that the research outcomes of the museums in Rotterdam be recorded in a separate report by historian Dr. A.J. Bonke: De herkomst van de aanwinsten van de Rotterdamse gemeentemusea 1940-1948 (The Provenances of the Acquisitions of the Municipal Museums in Rotterdam 1940-1948). Afterwards, he also wrote separate reports about specific art works or partial collections, such as Kunstwerken uit de voormalige Koenigs Collectie in Museum Boijmans Van Beuningen (Art Works from the former Koenigs Collection in Museum Boijmans van Beuningen), December 2001.
It turned out from the investigation of the acquisitions from 1940-1948 that the provenances of a number of art works from the museum collection were controversial. In 2006, Anita Hopmans, Head Curator Modern Art with the Netherlands Institute for Art History (RKD), wrote an extensive commentary on the provenances of two of these works: Omstreden bezit. Over de herkomst van twee werken van Jan Toorop in het Museum Boijmans: het schilderij De Theems (1885) en de tekening Godsvertrouwen (1907) (Disputed Ownership. On the Provenances of Two Works by Jan Toorop in the Boijmans Museum: the Painting Titled The Thames (1885) and the Drawing Known as Faith in God (1907)), December 2006 (in Dutch). This resulted in a publication from the series ‘Boijmans Studies’: A Hopmans, Verwerving en restitutie: de zaak Toorop / Acquisition and Restitution: the Toorop Case, Rotterdam 2008. Both works have been restituted to the heirs of Mr. E. Flersheim: the Toorop drawing in 2001, and the Toorop painting in 2009.
As a result of the outcomes of the investigations from 1998-1999 and of complementary provenance research, the museum at its own initiative restituted two drawings by Marius Bauer to the heirs of Ms. F.S.B. Ornstein (2000), a painting by Nicolaas van der Waay to the heirs of Mr. I.H. Leefsma (2001) and a drawing by George Hendrik Breitner to the heirs of Mr. E. de Vries (2001).