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Abstract Ultrasound‐directed self‐assembly (DSA) utilizes the acoustic radiation force associated with a standing ultrasound wave field to organize particles dispersed in a fluid medium into specific patterns. State‐of‐the‐art ultrasound DSA methods use single‐frequency ultrasound wave fields, which only allow organizing particles into simple, periodic patterns, or require a large number of ultrasound transducers to assemble complex patterns. In contrast, this work introduces multi‐frequency ultrasound wave fields to organize particles into complex patterns. A method is theoretically derived to determine the operating parameters (frequency, amplitude, phase) of any arrangement of ultrasound transducers, required to assemble spherical particles dispersed in a fluid medium into specific patterns, and experimentally validated for a system with two frequencies. The results show that multi‐frequency compared to single‐frequency ultrasound DSA enables the assembly of complex patterns of particles with substantially fewer ultrasound transducers. Additionally, the method does not incur a penalty in terms of accuracy, and it does not require custom hardware for each different pattern, thus offering reconfigurability, which contrasts, e.g., acoustic holography. Multi‐frequency ultrasound DSA can spur progress in a myriad of engineering applications, including the manufacturing of multi‐functional polymer matrix composite materials that derive their structural, electric, acoustic, or thermal properties from the spatial organization of particles in the matrix.