In this work, we present an integrated approach to synthesize process intensification systems with guaranteed flexibility and safety performances. The synthesis of intensified equipment/flowsheets is addressed through the Generalized Modular Representation Framework (GMF), which utilizes an aggregation of multifunctional mass/heat exchange modules to represent chemical processes. Thus, the optimal design options are investigated as mass- and heat-transfer opportunities using superstructure-based optimization techniques without a prepostulation of plausible configurations. To ensure that the designs can be operated under a specified range of uncertain parameters, a multiperiod GMF representation is developed based on the critical operating conditions identified by flexibility test. Risk assessment, accounting for equipment failure frequency and consequence severity, is incorporated as a constraint into this synthesis model to derive inherently safer designs. The resulting safely operable intensified systems, which are represented via phenomenological modules, are then identified as corresponding equipment-based flowsheets and validated with steady-state simulation. We demonstrate the proposed approach through a case study for the production of methyl tert-butyl ether. The results indicate that safety and operability considerations can result in significant changes in the structural and operating parameters of the optimal intensified design configuration.