Biological control is one of the effective methods for managing plant diseases in food production and quality. In fact, there is a growing trend to find new bio-sources, such as marine algae and vegetal by-products. In this study, pomegranate (Punica granatum) peel (S1) and Spirulina platensis (S2) alone and in combinations, pomegranate peel/Spirulina: 25%/75% (S3) and 50%/50% (S4) were evaluated for antimycotoxigenic and antiphytopathogenic fungal properties. The chemical composition (moisture, dry matter, protein, lipid and ash) as well as total polyphenols, flavonoids and anthocyanins content were evaluated in the four extracts. Using agar diffusion and broth microdilution methods, the anti Fusarium oxysporum, Fusarium culmorum, Fusarium graminearum, Aspergillus niger and Alternaria alternata activities were measured and their correlations with phytochemical content were evaluated. Interestingly, combinations between Spirulina at 75% and pomegranate peel at 25% (S3) have a significant impact (p < 0.05) on the antifungal activity compared to S1, S2 and S4. These findings underlie the effectiveness of biocontrols over standard fungicides and imply that existing methods can be further improved by synergistic effects while maintaining food safety in an eco-friendly manner.