The production of value-added bio-compounds from rejuvenated sources and their recruitment for healthcare services are paramount objectives in the agenda of white biotechnology. Hereupon, the current study focused on economic production of single cell oils (SCOs) from oleaginous fungi Alternaria sp. (A-OS) and Drechslera sp. (D-OS) using cheese whey waste stream, followed by their evaluation as antibiofilm and anticancer agents, for the first time. As a sole substrate for growth, the whey aided in lipid accumulation by 3.22 and 4.33 g/L, which representing 45.3 and 48.2% lipid content in Drechslera sp. (D-OS) and Alternaria sp. (A-OS), respectively. Meanwhile, a higher unsaturation degree was detected in A-OS by 62.18% comparing to 53.15% of D-OS, with advantageous presence of omega-6 poly unsaturated fatty acid by 22.67% and 15.04% for A-OS and D-OD, respectively, as revealed by GC-MS and FTIR characterization analysis. Interestingly, an eminent and significant (P ≤ 0.05) antibiofilm potency was observed in a dose-dependent modality upon employing both SCOs as antibiofilm agents. Whereas, 100 µg/mL of A-OS recorded superior inhibition of P. aeruginosa, S. aureus and C. albicans biofilms development by 84.10 ± 0.445, 90.37 ± 0.065 and 94.96 ± 0.21%, respectively. Whereas, D-OS (100 µg/mL) thwarted the biofilms of P. aeruginosa, S. aureus and C. albicans by 47.41 ± 2.83, 62.63 ± 5.82 and 78.67 ± 0.23%, correspondingly. Besides, the metabolic performance of cells within biofilm matrix, protein, carbohydrate contents and hydrophobicity of examined biofilms were also curtailed in a significant correlation with biofilm biomass (r ≥ 0.9). Further, as anticancer agents, D-OS recorded higher potency against A549 and CaCo-2 cell lines with IC50 values of 2.55 and 3.425% and SI values of 10.1 and 7.5, respectively. However, A-OS recorded 8.275% and 2.88 for IC50 and SI of Caco-2 cells, respectively. Additionally, A-OS activated caspase 3 by 64.23 ± 1.18% and 53.77 ± 0.995% more than D-OS (52.09 ± 0.222% and 49.72 ± 0.952%) in A549 and Caco-2 cells, respectively. Furthermore, the enzymes, which associated with cancer invasion, metastasis, and angiogenesis (i.e., MMP2 and MMP9) were strongly inhibited by A-OS with 18.58% and 8.295%, respectively as IC50 values; while D-OS results recorded 23.61% and 13.16%, respectively, which could be ascribed to the higher ω-6/ω-3 contents of A-OS. The promising results of the current study opens up the vision to employ SCOs as anti-infective nutraceuticals and in complementary/alternative therapy and prophylactic programs as well.