We introduce a new time-dependent lepto-hadronic model for blazar emission that takes into account the radiation emitted by secondary particles, such as pions and muons, from photo hadronic interactions. Starting from a baseline parameter set guided by a fit to the spectral energy distribution of the blazar 3C 279, we perform a parameter study to investigate the effects of perturbations of the input parameters to mimic different flaring events to study the resulting lightcurves in the optical, X-ray, high energy (HE: E > 100 MeV) and very-high-energy (VHE: E > 100 GeV) gamma-rays as well as the neutrino emission associated with charged-pion and muon decay. We find that flaring events from an increase in the efficiency of Fermi II acceleration will produce a positive correlation between all bandpasses and a marked plateau in the HE gamma-ray lightcurve. We also predict a distinctive dip in the HE lightcurve for perturbations caused by a change in the proton injection spectral index. These plateaus / dips could be a tell tale signature of hadronic models for perturbations that lead to more efficient acceleration of high energy protons in parameter regimes where pion and muon synchrotron emission is non-negligible.