Mushrooms play crucial roles as reservoirs of naturally occurring bioactive compounds. Among these, Cordyceps militaris is significant because of its well-established reputation for organoleptic excellence and positive health effects, which have led to its widespread commercialization. In contrast, the key properties of Paecilomyces variotii, an ectomycorrhizal symbiont, has received limited attention. In alignment with current research trends, the study of the mycelia and culture media of these mushrooms hold promise in identifying potential sources of valuable bioactive compounds. In the present study, we investigated C. militaris and P. variotii for their phenolic acids and sterols, assessing antioxidant capacity, anti-inflammatory effects, and anti-proliferative activity. Interestingly, P. variotii mycelia exhibited higher concentrations of ergosterol and phenolic compounds, with comparable levels observed in the fruiting bodies, along with superior antioxidant activity compared to that of C. militaris. In contrast, C. militaris mycelia demonstrated anti-inflammatory effects (which were absent in P. variotii mycelia) and cytotoxicity comparable to, and at times exceeding, that of its fruiting bodies (in contrast to P. variotii). In addition, the species analyzed in this study displayed variations in growth rates and mycelial production, which merit consideration for potential future applications and further study.