Because of their higher efficiency of energy utilization, heat-integrated column systems have been widely used in the chemical industry. However, the heat integration leads to difficulties in startup of such columns, i.e. a long startup time, and thus considerable costs will result. In this work, a study consisting of modelling, simulation, optimization and experimental verification is carried out to develop optimal operation strategies for heat-integrated columns to reduce the startup time. A pilot two-pressure column system with bubble-cap trays is considered. More than 35% of the startup time can be reduced in comparison to conventional startup procedure. Heuristics for startup operation of such processes are suggested.