Microalgae and cyanobacteria represent a largely unexplored source of bioactive compounds, but systematic screening of extensive strain collections is limited by the cost and complexity of conventional chemical and pharmacological characterization. Here, we evaluated a scalable functional screening strategy integrating human cell-based gene expression profiling, quantitative molecular pathway analysis, and direct cytotoxicity testing to prioritize bioactive microalgal and cyanobacterial extracts for subsequent investigation. Forty-eight extracts were screened using HL-60 human leukemia cells, and eight demonstrated detectable cytotoxic activity. Pathway-based prediction showed 92% agreement with direct cytotoxicity measurements. To assess whether pathway profiling could provide information on mechanisms of action, we performed an in-depth analysis of the most active sp. SBV-48 extract and the control antimicrobial peptide Polyphemusin III. The inferred pathway responses were consistent with their previously reported mechanisms of cytotoxicity. Fractionation and chemical characterization of the sp. SBV-48 extract identified Cryptophycin-1 as its major cytotoxic component, illustrating the intended sequential workflow from primary screening to characterization of prioritized hits. In addition, previously unreported cytotoxic activity against HL-60 cells was detected in three Desmidiales strains belonging to the genera , , and , which showed partially convergent pathway-level responses. Overall, the proposed approach provides a cost-effective first-stage strategy for functional screening and prioritization of complex microalgal extracts, allowing resource-intensive chemical characterization and broader pharmacological validation to be focused on the most promising candidates.