Natural metabolites from beneficial fungi were recognized for their potential to inhibit multidrug-resistant human and plant fungal pathogens. The present study describes the isolation, metabolite profiling, antibacterial, and antifungal, antioxidant, and anticancer activities of soil fungi. Among the 17 isolates, the AK-7 isolate was selected based on the primary screening. Further, the identification of isolate AK-7 was performed by 18S rRNA sequencing and identified as Penicillium limosum (with 99.90% similarity). Additionally, the ethyl acetate extract of the Penicillium limosum strain AK-7 (AK-7 extract) was characterized by Fourier Transform Infrared Spectroscopy (FTIR) and a Gas Chromatography-Mass Spectroscopy (GC-MS) analysis, and the results showed different functional groups and bioactive metabolites. Consequently, a secondary screening of antibacterial activity by the agar well diffusion method showed significant antibacterial activity against Gram-negative and Gram-positive bacterial pathogens. The AK-7 extract exhibited notable antifungal activity by a food poisoning method and showed maximum inhibition of 77.84 ± 1.62%, 56.42 ± 1.27%, and 37.96 ± 1.84% against Cercospora canescens, Fusarium sambucinum and Sclerotium rolfsii phytopathogens. Consequently, the AK-7 extract showed significant antioxidant activity against DPPH and ABTS•+ free radicals with IC50 values of 59.084 μg/mL and 73.36 μg/mL. Further, the anticancer activity of the AK-7 extract against the human ovarian teratocarcinoma (PA-1) cell line was tested by MTT and Annexin V flow cytometry. The results showed a dose-dependent reduction in cell viability and exhibited apoptosis with an IC50 value of 82.04 μg/mL. The study highlights the potential of the Penicillium limosum strain AK-7 as a source of active metabolites and natural antibacterial, antifungal, antioxidant, and anticancer agent, and it could be an excellent alternative for pharmaceutical and agricultural sectors.