Cu100−xCox thin films have been obtained by sputtering (x = 3, 9) and sputter gas aggregation (x = 2.5, 7.5) and subsequent annealing at 400 °C for 1 h. We have studied their structural, magnetic, and magnetotransport properties, both for the as-deposited and annealed samples, confirming the important role of the fabrication method in the properties. The magnetic measurements and the fitting of the hysteresis loops evidence that as-deposited samples consist of superparamagnetic (SPM) and/or ferromagnetic clusters, but in the samples obtained by gas aggregation the clusters are greater (with ferromagnetic behavior at room temperature) whereas in the samples obtained by sputtering, the clusters are smaller and there are also diluted Co atoms in the Cu matrix. The annealing affects negligibly the samples obtained by gas aggregation, but the ones obtained by sputtering are more affected, appearing greater clusters. This behavior is also reflected in the magnetoresistance (MR) measurements of the samples, with different shapes of the MR curves depending on the preparation method: more lineal in the whole range for sputtering, saturation at low fields (about 10 kOe) for gas aggregation. Finally, a Kondo-like minimum in the resistance versus temperature is found in the samples obtained by sputtering, affected by the magnetic field and the annealing. The observed Kondo-like behavior and the influence of annealing on a Kondo-like minimum in sputtered thin films have been attributed to the presence of diluted Co atoms in the Cu matrix and the Co precipitations from the Co–Cu solid solution upon annealing respectively.