Microalgae are photosynthetic microorganisms that have increasingly attracted interest in the last decade due to their potential for industrial applications. One crucial aspect for the industrial-scale valorisation of algae biomass concerns the quality control during its preservation before being treated to obtain the end-product. Monitoring biomass quality is essential and can be potentially accomplished with the aid of specific biochemical indicators called biomarkers. In this context, the main aim of this work was to identify potential indicators of microalgae biomass viability that could be used as markers of its quality during storage/preservation for commercial operations. The health status of a suspension of Chlamydomonas nivalis was assessed at 4 ºC and 25 ºC during 10 days of storage. The use of the pulse-amplitude-modulation technique, based on chlorophyll fluorescence, was a valuable indicator of the culture viability. The measurement of DNA and of chlorophyll in the supernatant, indicative of cell lysis, also provided satisfactory results; in the case of the DNA, the limit of detection was 3.9 µg DNA·mL−1. The effect of different concentrations of a well-known and cheap preservative, acetic acid, was also evaluated at 4 ºC. This work identified three suitable biomarkers to be used as rapid indicators of the quality of the microalgal suspension prior to its reception for biorefinery activities.