The whistling induced by a low-Mach turbulent flow through a deep axisymmetric cavity in a duct is investigated theoretically and experimentally. The experiments include acoustic measurements and stereoscopic particle image velocimetry (PIV). The paper focuses on the effect of a mean swirl on the dynamics of the azimuthal aeroacoustic modes. The mean swirl in the cavity has two origins: one component is imposed by a controlled tangential air injection upstream of the cavity, and the other component spontaneously arises under the action of the self-sustained azimuthal aeroacoustic mode, as explained in the companion paper, Part 1 (Faure-Beaulieu, Xiong, Pedergnana & Noiray, J. Fluid Mech., vol. 971, 2023, A21). Experiments show that the dynamics of the aeroacoustic wave is influenced by the imposed swirl. In particular, the spinning wave propagating against the swirl is promoted. To explain this, a linear perturbation analysis is performed around an incompressible mean swirling flow obtained from RANS simulations. It reveals that the dominant shear layer modes of azimuthal order 1 and −1 involved in the whistling phenomenon are helical modes winding respectively with and against the swirl, and spinning respectively in counterswirl and co-swirl directions. The counterswirl hydrodynamic mode is the least damped of the two, which is in agreement with the experimental observations. Finally, a low-order model based on the wave equation is derived. With only a few parameters, it fully reproduces the experimental observations for a wide range of imposed swirl intensity in the duct flow, and it allows us to disentangle the mechanisms responsible for this complex aeroacoustic instability.