A three-level atom in Λ configuration is reduced to an effective two-level system, under appropriate conditions, and its PT symmetric properties are investigated. This effective qubit system, when subjected to a beam-splitter type of interaction, provides the scope of directly (indirectly) probing the nonclassical properties of the output (input) state. Here, we study nonclassical properties of the output state by using some well-known measures of nonclassical correlations like the measurement-induced disturbance, concurrence, and negativity. The nonclassical features are found to enhance in the PT symmetric (PTS) phase compared to the PT symmetry broken (PTB) phase. Further, the output ports of the beam splitter are subjected to different quantum noise channels, both non-Markovian, e.g., random telegraph noise as well as Markovian, e.g., phase damping and amplitude damping noise. The application of noise channels is found to decrease the degree of nonclassicality, though continuing to exhibit distinct behavior in PTS and PTB phases, with the dominant behavior appearing in the former case. Further, the results are compared with the case when dynamics is governed by a Hermitian Hamiltonian. This allows one to demarcate the contributions to nonclassicality from different types of dynamics. © 2019 American Physical Society. ©2019 American Physical Society.