Whilst a wealth of Thomson buildings remain there are also a significant number that have been tragically lost over the years. The reasons for these losses are several, from Thomson demolishing his own buildings – as with the Scottish Exhibition Rooms on Bath Street, through to bombing during World War II – as with Queens Park Church. The most common reason for the loss of these buildings however was redevelopment during the 1960s and 70s.

The losses were primarily tenemental properties spread throughout the city, however also included were two hotels, a printing works, a sculpture yard and two churches; Chalmers Memorial Free Church in the Gorbals and Queen’s Park Church.