The early stages of mussel farming are often inefficient with a large proportion of seed (spat) typically lost early in the production cycle. An effective approach for decreasing such losses is to grow spat to larger sizes in nursery systems prior to seeding. However, for such an approach to be commercially viable, spat must first be separated from their settlement substrates into a single seed format, that is, singulated. This study investigated the efficacy of three commercial protease enzymes (Enzidase PAP, PXT and BAP) and chlorine (NaOCl) in singulating Greenshell mussel (Perna canaliculus) spat from spat‐collector ropes. Two distinct experiments involved immersing segments of spat collector rope in seawater solutions with varying concentrations (2.5% or 5%) of each enzyme or chlorine (NaOCl) for different exposure times (10, 30 and 60 min for enzymes; 2 and 5 min for chlorine). After the singulation experiments, all spat were recovered with sieves and reintroduced into the tanks with renewed seawater. After 24 h of rearing, the recovery of alive spat was measured. Results indicate that in Experiment 1, involving spat ∼5 mm in size, the singulation rate was up to 65% for protease enzymes (i.e., in the case of 5% PAP at 30 min) and 61% for chlorine (i.e., at 5% for 2 min). In Experiment 2, involving spat ∼1.5 mm in size, the singulation rate was up to 85% for protease enzymes (i.e., in the case of 5% PXT for 60 min) and 78% for chlorine (i.e., of 2.5% for 5 min). However, these treatments generally resulted in elevated spat mortality, which was exacerbated by increasing concentrations and exposure times, resulting in recovery rates of up to 35% (i.e., for 2.5% PAP for 30 min) in Experiment 1 and 26.0% (i.e., for 5% chlorine for 2 min) in Experiment 2. These findings emphasise the necessity for consideration of chemical concentrations and exposure times to optimise the singulation process while highlighting challenges in achieving high post‐singulation survival rates. These insights contribute to ongoing efforts aimed at improving the efficiency and sustainability of mussel farming practices, demonstrating the potential utility of protease enzymes and chlorination in singulating spat from settlement substrate prior to their transfer to nursery systems for further ongrowing.