We study an atomic Josephson junction (AJJ) in the presence of two interacting Bose–Einstein condensates (BECs) confined in a double-well trap. We assume that bosons of different species interact with each other. The macroscopic wavefunctions of the two components obey a system of two 3D coupled Gross–Pitaevskii equations (GPEs). We write the Lagrangian of the system, and from this we derive a system of coupled ordinary differential equations (ODEs), for which the coupled pendula represent the mechanical analogues. These differential equations control the dynamical behaviour of the fractional imbalance and of the relative phase of each bosonic component. We perform the stability analysis around the points which preserve the symmetry and get an analytical formula for the oscillation frequency around the stable points. Such a formula could be used as an indirect measure of the inter-species s-wave scattering length. We also study the oscillations of each fractional imbalance around zero and nonzero—the macroscopic quantum self-trapping (MQST)—time averaged values. For different values of the inter-species interaction amplitude, we carry out this study both by directly solving the two GPEs and by solving the corresponding coupled pendula equations. We show that, under certain conditions, the predictions of these two approaches are in good agreement. Moreover, we calculate the crossover value of the inter-species interaction amplitude which signals the onset of MQST.