The usage of a modified Z-scan setup for the study of optical nonlinearities of bis-phthalocyanines is discussed. The setup leads to the selection of the pure electronic nonlinear optical response purged from other possible contributions such as molecular reorientation or thermal effects. The described experimental method is based on the capability to extract the instantaneous nonlinear response of the sample, by monitoring and managing cumulative effects and taking full advantage of the large number of probing laser pulses. This kind of approach has been applied on some sandwich-type metal bis-phthalocyanines confirming its potential for an in-depth analysis of the nonlinear response of such molecules. First results on titanium, niobium and tin bis-phthalocyanines provide information on the role of the conjugation length in their nonlinear optical response.