We study the phase-space concentration of the so-called generalized metaplectic operators whose main examples are Schrödinger equations with bounded perturbations. To reach this goal, we perform a so-called $${\mathcal {A}}$$
A
-Wigner analysis of the previous equations, as started in Part I, cf. Cordero and Rodino (Appl Comput Harmon Anal 58:85–123, 2022). Namely, the classical Wigner distribution is extended by considering a class of time–frequency representations constructed as images of metaplectic operators acting on symplectic matrices $${\mathcal {A}}\in Sp(2d,\mathbb {R})$$
A
∈
S
p
(
2
d
,
R
)
. Sub-classes of these representations, related to covariant symplectic matrices, reveal to be particularly suited for the time–frequency study of the Schrödinger evolution. This testifies the effectiveness of this approach for such equations, highlighted by the development of a related wave front set. We first study the properties of $${\mathcal {A}}$$
A
-Wigner representations and related pseudodifferential operators needed for our goal. This approach paves the way to new quantization procedures. As a byproduct, we introduce new quasi-algebras of generalized metaplectic operators containing Schrödinger equations with more general potentials, extending the results contained in the previous works (Cordero et al. in J Math Pures Appl 99(2):219–233, 2013, J Math Phys 55(8):081506, 2014).