Actinobacteria are known for their production of bioactive specialized metabolites, but still under-exploited due to silent biosynthetic gene clusters (BGCs) not expressed in conventional laboratory cultures conditions. In this study, three marine-derived actinobacteria were cultured using the one strain many compounds method (OSMAC) to explore the real potential of these microorganisms. Salinispora arenicola (SH-78) and two Micromonospora sp. (SH-82 and SH-57) were grown under varying parameters such as time, medium composition, and culture support. The microbial extracts produced were chemically screened by high-resolution analysis (HRMS/MS). The data were used to build ion identity molecular networks (IIMN) and annotate the specialized metabolites detected. A selection of extracts was biologically screened for their cytotoxic and antiplasmodial activities. The IIMNs and the annotations produced were used to assess the impact of culture parameters on the metabolomic diversity of the selected actinobacteria and highlight the presence of unique molecules to specific culture conditions. Micromonospora sp. SH-57 produced a greater quantity of metabolites in liquid culture, with higher associated biological activity. The method employed allowed to explore deeper the specialized metabolites production and to identify the best culture conditions to produce bioactive natural products.