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There is growing evidence that marine microorganisms may influence cloud cover over the ocean through their impact on sea spray and trace gas emissions, further forming cloud droplets or ice crystals. However, evidence of a robust causal relationship based on observations is still pending. In this study, we use 4 years of multi‐instrument satellite data to segregate low‐level clouds into ice‐containing and liquid‐water clouds to obtain clear relationships between cloud types and ocean biological tracers, especially with nanophytoplankton cell abundances. Results suggest that microorganisms may be involved in compensating effects on cloud properties, increasing the frequency of occurrence of warm‐liquid clouds, and decreasing the occurrence of ice‐containing clouds in most regions during springtime. The relationships observed in most regions do not apply to the South Pacific Ocean in the 40°S–50°S latitude band. These results shed light on overlooked potential compensating effects of ocean microorganisms on cloud cover. Plain Language Summary: Climate is governed by interactions between the ocean and the atmosphere. While physical interactions such as exchanges of heat and water vapor are fairly well understood, the role of biology, that is, the living marine microorganisms, on atmospheric processes, is a lot more complex. For instance, marine microorganisms may influence the number and the chemical composition of sea sprays and also emit trace gasses that will form tiny particles. Sea sprays and newly formed particles can then serve as nuclei on which cloud droplets or ice crystals form, therefore influencing cloud properties and climate. These chains of processes are theoretical, and there are few clear linkages between ocean biology and cloud properties derived from observational data. This study uses new satellite retrievals to establish relationships between cloud phase occurrence (ice, warm‐liquid, mixed‐phase or supercooled‐liquid clouds) and the biological activity of the ocean in different regions of the southern ocean. For a given month, locations of higher abundance of phytoplankton corresponds to a higher warm‐liquid cloud cover but lower ice cloud cover. These results suggest compensating effects of marine microorganisms on cloud lifetime via their potential to impact the formation of particles able to become water droplets or ice crystals. Key Points: Nanophytoplankton biomass shows more relations to cloud occurrences than Chlorophyll‐a or Particulate Organic Carbon concentrationsHigher nanophytoplankon abundance is positively linked to warm‐liquid cloud frequency of occurrence in spring in most regions of 40°S–60°SHigher nanophytoplankton abundance is linked to a decrease in the ice‐containing cloud frequency of occurrence in most regions [ABSTRACT FROM AUTHOR]