Cadophora luteo-olivacea, Phaeoacremonium minimum, and Pseudophaeomoniella oleicola have been associated with branch dieback, shoot blight, and vascular wilt in super-high-density olive plantations in Spain. In this study, the effects of the interaction between these three fungal species on the disease progression were evaluated through multi-infections inoculated by spore suspensions or mycelial plugs in olive plants of cultivar Arbequina. The susceptibility of six olive cultivars was also evaluated against these three pathogens by single inoculations with conidial suspensions. The detection and inoculum quantification of each fungal species from coinfected plant tissues or from inoculated plants of different cultivars was conducted by qPCR, using species-specific primers. In addition, a species-specific primer to identify Ps. oleicola was developed in this study. In the multi-infections experiment with conidial suspensions, lesions on olive infected simultaneously with all three species were larger than those on plants coinfected by two species, which were, in turn, larger than those inoculated by a single species. However, when inoculations were conducted with mycelial plugs, C. luteo-olivacea caused larger lesions than those in coinfected plants. The quantification of these fungi through qPCR suggests that their interaction during coinfections significantly alters their relative abundance, potentially impacting their aggressiveness. Regarding the cultivar resistance experiment, the most susceptible cultivar to the disease was ‘Koroneiki’, followed by ‘Arbequina’ and ‘Picual’. In all the samples, the detection of C. luteo-olivacea was an order of magnitude lower than that of the other fungal species. Nevertheless, the relative quantification of fungi by qPCR, despite being useful to detect the presence of the pathogen, does not correlate with the lesions observed.