Mechanical separation of co-digestate removes dry matter (DM) and phosphorous (P) from digestate effectively but is less capable at removing nitrogen (N) and potash (K). Adding flocculants can enhance separator efficiency. However, information on the use of chitosan as flocculant for co-digestate and its effects on amended slurry application to soil is scarce. This study undertook a series of trial and error tests to identify the optimal chitosan dose to be applied to co-digestate. Four chitosan doses were evaluated: 120 (Dose 1), 240 (Dose 2), 360 (Dose 3), and 480 (Dose 4) mL L −1 of co-digestate. After optimal dose application, centrifugation was employed to separate the co-digestate (centrifugation tests). We used simple separation indices to evaluate the effectiveness of chitosan addition prior to centrifuge usage. Dose optimization tests results indicated that incremental doses of chitosan had no effect (p > 0.05) on total N and it decreased (p < 0.05) total P removal to solids. Dose 3 showed a superior effect based on the physical characteristics evaluated and on the DM content of the fractions produced. Centrifugation tests results showed chitosan increased (p < 0.05) centrifugation efficiency for K, copper (Cu), and zinc (Zn) (75, 36, and 51%, respectively) and had no effect on total N or P. The major findings show that the use of natural and relatively cheap polymer chitosan improves the efficacy of co-digestate centrifugation with respect to K, Cu, and Zn, lowering their load to arable land once a solid fraction is applied.