Clozapine has shown signs of effectiveness in treating symptoms of schizoaffective disorder, although little research has been carried out to specifically assess this question. The objective of this current work was to analyse the mood-stabilising effectiveness and tolerability of clozapine in patients with schizoaffective disorder. This was a prospective, longitudinal, and quasi-experimental trial with three months of follow-up in patients with refractory schizoaffective disorder (PANSS score exceeding 80). Clinical response was evaluated through monthly visits using the YMRS, MADRS, CDSS, CGI-S and UKU. Twenty-seven participants (63% men, 37% women) with a mean age of 32.56 years were included. Clozapine significantly reduced the symptoms of mania, as measured by the YMRS (pre-treatment: 16.19, post-treatment: 0.67; p < 0.01) as well as the symptoms of depression, quantified with the CDSS (pre-treatment: 6.11, post-treatment: 0.67; p < 0.01), MADRS (pre-treatment: 9.56, post-treatment: 1.07; p < 0.01), and CGI-S (pre-treatment: 4.74, post-treatment: 1.15; p < 0.01). The prescription of clozapine significantly reduced the average daily dose of neuroleptics, measured in mg of chlorpromazine (pre-treatment: 1253.55, post-treatment: 742.59; p < 0.01) and hypnosedatives, measured in mg of diazepam (pre-treatment: 33.88, post-treatment: 5.74; p < 0.05) required in these patients. Patient-perceived tolerability, measured with the UKU, also improved during follow-up (pre-treatment: 12.89, post-treatment: 8.14; p < 0.01). The efficacy of clozapine was significant for the affective symptoms of schizoaffective disorder, thereby improving patient tolerability and permitting reductions in the other medications the patients used.