A strong start to the 2008–09 league campaign saw the club sitting top of the table in October. At the same time, Chisholm was linked with the vacant position at Dundee, but Davie Rae refused Chisholm permission to talk to the "Dark Blues". This coincided with Queens losing form, as they gained only three draws from the next 12 games placing them only one place above bottom. Their form improved in the latter part of the season and the club finished in mid-table.