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The study of the magnetic properties of Co nanoparticles (with an average diameter of 10.3 nm) grown using a gas-phase aggregation source and embedded in Au and V matrices is presented. We investigate how the matrix, the number of embedded nanoparticles (counted by coverage percentage), the interparticle interactions and the complex nanoparticles/matrix interface structure define the magnetic properties of the studied systems. A threshold coverage of 3.5% of a monolayer was found in both studied systems: below this coverage, nanoparticles behave as an assembly of independent single-domain magnetic entities with uniaxial anisotropy. Above the threshold it is found that the magnetic behavior of the systems is more matrix dependent. While magnetic relaxation and Henkel plots measurements stress the importance of the dipolar interactions and the formation of coherent clusters in the case of the Au matrix, the magnetic behavior of cobalt clusters embedded in the vanadium matrix is explained through the formation of a spin glass-like state at the V-Co interface that screens the magnetic interactions between NPs.