A new scheme has been developed for the confined synthesis of silicalite nanocrystals. The scheme involves: (1) Prepare a clear solution that is known to produce colloidal TPA-silicalite upon extended hydrothermal reaction. (2) Subject the solution to hydrothermal condition but stop before the appearance of colloidal silicalite. (3) Protect the TPA-silicalite precursor nanoparticles with cationic surfactant and collect them as flocculated mass. (4) Convert the precursor/surfactant hybrid into nanocrystals via high temperature steaming. It was found that an intermediate dilution during the hydrothermal step helped to delay the appearance of colloidal silicalite, and to produce more precursor nanoparticles. A steaming temperature of 150 °C was also found enough to convert the collected precursor into nanocrystals. The obtained nanocrystals were smaller than 30 nm with good XRD and IR crystallinity, which survived after 550 °C calcination.