Layered materials, such as MoS2, have a wide range of potential applications due to the properties of a single layer, which often differ from the bulk material. They are of particular interest as ultrathin diffusion barriers in semiconductor device interconnects and as supports for low-dimensional metal catalysts. Understanding the interaction between metals and the MoS2 monolayer is of great importance when selecting systems for specific applications. In previous studies the focus has been largely on the strength of the interaction between a single atom or a nanoparticle of a range of metals, which has created a significant knowledge gap in understanding thin film nucleation on 2D materials. In this paper, we present a density functional theory (DFT) study of the adsorption of small Co and Ru structures, with up to four atoms, on a monolayer of MoS2. We explore how the metal–substrate and metal–metal interactions contribute to the stability of metal clusters on MoS2, and how these interactions change in the presence of a sulfur vacancy, to develop insight to allow for a prediction of thin film morphology. The strength of interaction between the metals and MoS2 is in the order Co > Ru. The competition between metal–substrate and metal–metal interaction allows us to conclude that 2D structures should be preferred for Co on MoS2, while Ru prefers 3D structures on MoS2. However, the presence of a sulfur vacancy decreases the metal–metal interaction, indicating that with controlled surface modification 2D Ru structures could be achieved. Based on this understanding, we propose Co on MoS2 as a suitable candidate for advanced interconnects, while Ru on MoS2 is more suited to catalysis applications.