We develop a theoretical framework to describe the scattering of photons against a two-level quantum emitter with arbitrary correlated dephasing noise. This is particularly relevant to waveguide-QED setups with solid-state emitters, such as superconducting qubits or quantum dots, which couple to complex dephasing environments in addition to the propagating photons along the waveguide. Combining input-output theory and stochastic methods, we predict the effect of correlated dephasing in single-photon transmission experiments with weak coherent inputs. We discuss homodyne detection and photon counting of the scattered photons and show that both measurements give the modulus and phase of the single-photon transmittance despite the presence of noise and dissipation. In addition, we demonstrate that these spectroscopic measurements contain the same information as standard time-resolved Ramsey interferometry, and thus they can be used to fully characterize the noise correlations without direct access to the emitter. The method is exemplified with paradigmatic correlated dephasing models such as colored Gaussian noise, white noise, telegraph noise, and 1/fnoise, as typically encountered in solid-state environments.quantum emitter in addition to the dissipative dynamics due to the coupling to photons in the waveguide. We then relate the correlations in that noise to the average scattering matrix of individual photons and coherent wavepackets, and develop strategies to extract those correlations from actual experiments, in conjunction with earlier approaches to scattering tomography [49].The paper and our main results are organized as follows. In section 2 we introduce the model for a noisy twolevel emitter in a waveguide. We describe dephasing noise as a stationary stochastic process Δ(t) and derive the stochastic input-output equations. In section 3, we review the standard procedure of Ramsey interferometry and show how to quantify the noise correlations via the Ramsey envelope C f (t). We also introduce paradigmatic correlated noise models, which will be essential to understand the scattering results in the next sections. In particular, section 4 shows that the same information provided by Ramsey spectroscopy can be obtained from single-photon scattering experiments, where we only manipulate the qubit through the scattered photons. We solve the stochastic input-output equations for a qubit that interacts with a single propagating photon, and show that the averaged single-photon scattering matrix can be related one-to-one to the Ramsey envelope. We also discuss analytical predictions for scattering under realistic dephasing models such as colored Gaussian noise and 1/f noise. We show how the noise correlations modify the spectral lineshapes on each case, recovering simple limits such as the Lorentzian profiles that are fitted in most waveguide-QED experiments. Section 5 generalizes these ideas, showing how to measure the averaged scattering matrix using weak coherent state inputs together with homodyne or photon countin...