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We present a methodology for constructing modified gravity (MG) constrained simulations of the local Universe using positions and peculiar velocities from the CosmicFlows data set. Our analysis focuses on the following MG models: the normal branch of the Dvali-Gabadadze-Porrati (nDGP) model and Hu-Sawicki $f(R)$ model. We develop a model independent methodology for constructing constrained simulations with any given power spectra and numerically calculated linear growth functions. Initial conditions (ICs) for a set of constrained simulations are constructed for the standard cosmological model $Λ$CDM and the MG models. Differences between the model's reconstructed Wiener filtered density and the resultant simulation density are presented showing the importance for the generation of MG constrained ICs to study the subtle effects of MG in the local Universe. These are the first MG constrained simulations ever produced. The current work paves the way to improved approximate methods for models with scale-dependent growth functions, such as $f(R)$, and for high-resolution hydrodynamical MG zoom-in simulations of the local Universe.