Whooping cough is a respiratory disease resulting from Bordetella pertussis infection that remains a globally significant cause of vaccine-preventable deaths. As a major virulence factor, the adenylyl cyclase toxin (ACT) of Bordetella pertussis (CyaA) has evolved a unique mode of activation by host cell calmodulin (CaM), thereby making it a potential target for the design of novel therapeutics. Currently, no high-resolution structure of intact CaM bound to CyaA exists, so the molecular pathways controlling enzymatic activation remain unclear. Previously, we have identified unique sites of intermolecular association between CyaA and CaM that directly impact CaM's structure, metal-binding properties, and conformational stability. In this study, we utilized site-directed mutagenesis, biophysical, and biochemical techniques to investigate the roles of metal-binding and CaM-dependent interactions in regulating CyaA structure and function. Site-specific mutations mapping to metal-binding site I or II of CaM reduced CyaA binding affinity and cAMP production without significantly altering CaM conformation. Moreover, inactivation of sites I or II in CaM modulated the global conformation of the CaM/CyaA complex in a metal-dependent manner. In the absence of CaM, CyaA exhibited multiple thermal transitions during unfolding experiments, but domain-specific interactions with wild-type or mutant CaM increased the thermal stability of the complex. Together, these data support that CaM-dependent CyaA activation occurs by novel structural mechanisms. This study sheds light on the molecular details of CaM-regulated ACTs, knowledge which may be exploited in the rationale design of inhibitory compounds.