The specifics of industrial enterprises’ functioning in the construction sector of the Russian economy are of particular interest and have been a subject of active discussion over the past years. This article analyzes functioning of the construction complex companies in the context of new global challenges associated with the crisis phenomena in 2020 – the fall in oil prices and the coronavirus infection, as well as the transition to remote operation during the pandemic of basic economic branches. Nowadays, it is especially important to assess reserves for sustainable innovative development of industrial enterprises and predict consequences of the crisis phenomena. The authors investigate some organization forms for the innovative process, determine key efficiency factors of enterprises’ innovative activity and propose ways for its improvement.