The main challenge of astaxanthin extraction is to provide an eco-friendly method of extraction instead of chemical methods that harm human health. This study provided an eco-friendly method for astaxanthin extraction using two bacterial and fungal probiotics (Bifidobacterium lactis, Lactobacillus lactis, Candida utilis, and Saccharomyces cerevisiae, respectively) and determined the astaxanthin concentration by high-performance liquid chromatography (HPLC) analysis. The results showed that the highest concentration was obtained by S. cerevisiae (45.69 µg/g). Several biological tests were done on the exoskeleton containing astaxanthin of crawfish. Antifungal activity was effective against C. utilis (inhibition zone is 12.3 ± 0.5 mm). The scavenging percentage of 2,2-diphenyl-1-picrylhydrazyl (DPPH scavenging percentage) was 72.1% at 1000 µg/mL concentration of exoskeleton containing astaxanthin. The Hemolysis inhibition percentage was 65% at the same concentration used previously. Furthermore, the IC50 value of human liver cancer cell line (HepG2), human hepatocellular carcinoma (HCT), and breast cancer cell line MCF-7 were 24 µg/mL, 11 µg/mL, and 9.5 µg/mL, respectively. The least cell viability percentage was 19% (using breast cancer cell line (MCF-7)) at 100 µg/mL of exoskeleton containing astaxanthin. Thus, using microorganisms can be an alternative and promising way of astaxanthin extraction. Furthermore, purification of extracted astaxanthin is essential for medical applications.