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Recent advances in two-dimensional (2D) materials have led to the renewed interest in intercalation as a powerful fabrication and processing tool. Intercalation is an effective method of modifying the interlayer interactions, doping 2D materials, modifying their electronic structure or even converting them into starkly different new structures or phases. Herein, we discuss different methods of intercalation and provide a comprehensive review of various roles and applications of intercalation in next‐generation energy storage, optoelectronics, thermoelectrics, catalysis, etc. The recent progress in intercalation effects on crystal structure and structural phase transitions, including the emergence of quantum phases are also reviewed.