MCM-56 is a unique zeolite with MWW topology consisting of 2.5 nm thick mono-layers. It is formed as an intermediate converting into the 3D MWW zeolite, MCM-49. It is attractive for catalysis with well documented high activity for hydrocarbon conversions but as a transient product MCM-56 presents novel challenges with regard to synthesis and activation. This work describes application of IR spectroscopy to monitor MCM-56 formation by investigating solid products obtained at different times during hydrothermal synthesis with hexamethyleneimine as template. We identified a unique double band in the range 500–600 cm−1, which can be assigned to skeletal vibrations of D6R units, that appears upon formation of MWW framework and can be used for quantitative determination of its content in a sample. The integrated intensity correlates well with XRD crystallinity, micropore volume and Brønsted acid sites concentration. FTIR approach allows facile and fast measurement and therefore may complement and possibly supplant XRD and porosity for reliable quality control in the course of MCM-56 crystallization, e.g. for the purpose of rapid termination of the synthesis at ‘the optimal time’.