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Abstract Targeting DNA payloads into human (h)iPSCs involves multiple time-consuming, inefficient steps that must be repeated for each construct. Here, we present STRAIGHT-IN Dual, which enables simultaneous, allele-specific, single-copy integration of two DNA payloads with 100% efficiency within one week. Notably, STRAIGHT-IN Dual leverages the STRAIGHT-IN platform to allow near-scarless cargo integration, facilitating the recycling of components for subsequent cellular modifications. Using STRAIGHT-IN Dual, we investigated how promoter choice and gene syntax influence transgene silencing, demonstrating the impact these design features have on reporter gene expression and forward programming of hiPSCs into neurons, motor neurons, and endothelial cells. Furthermore, we designed a grazoprevir-inducible synZiFTR system to complement the widely used tetracycline-inducible system, providing independent, tunable, and temporally controlled expression of different transcription factors within the same cell. The unprecedented efficiency and speed with which STRAIGHT-IN Dual generates homogenous genetically engineered hiPSC populations represents a major advancement for synthetic biology in stem cell applications and opens opportunities for precision cell engineering.