He served as a Parliamentary Under-Secretary of State for Scotland responsible for local government and transport minister for a few months in 1997; but resigned over single parent benefit cuts.

He remained an MP until 2001, when he stood down from the House of Commons in order to concentrate on the Scottish Parliament, to which he was elected in 1999 for the same constituency.

[2] As Minister for Communities, Chisholm oversaw investment in the building of affordable homes,[3][4] approved a proposal from Fife Council for a moratorium on council house sales in order to maintain the supply of affordable housing,[5] developed reforms of planning policy to protect green spaces,[6] and extended the Central Heating Programme and Warm Deal to provide and refurbish heating systems for pensioners.

[8] He subsequently resigned on 21 December 2006 after supporting a motion passed by the Scottish National Party that opposed the replacement of the nuclear submarines.

[9] On 17 September 2007, Chisholm was appointed Shadow Minister for Culture and External Affairs by new Scottish Labour leader, Wendy Alexander.