Multimode photon-subtraction provides an experimentally feasible option to construct large non-Gaussian quantum states in continuous-variable quantum optics. The non-Gaussian features of the state can lead towards the more exotic aspects of quantum theory, such as negativity of the Wigner function. However, the pay-off for states with such delicate quantum properties is their sensitivity to decoherence. In this paper, we present a general model that treats the most important source of decoherence in a purely optical setting: losses. We use the framework of open quantum systems and master equations to describe losses in n-photon-subtracted multimode states, where each photon can be subtracted in an arbitrary mode. As a main result, we find that mode-dependent losses and photon-subtraction generally do not commute. In particular, the losses do not only reduce the purity of the state, they also change the modal structure of its non-Gaussian features. We then conduct a detailed study of single-photon subtraction from a multimode Gaussian state, which is a setting that lies within the reach of present-day experiments. arXiv:1905.06755v1 [quant-ph]