Atmospheric radiation is primarily produced during the interaction of high-energy cosmic rays with the atmosphere. At typical flight altitudes, the integrated flux of secondary particles can easily reach up to hundreds of thousands per square meter per second. This ionizing radiation constitutes a risk factor for radiation exposure for crew members, passengers, and avionics during commercial flights. Different methods have been implemented in the past two decades to estimate the dose during commercial flights. The main advantage of these methods is their low computing demand, as they rely on precalculated libraries and interpolate or extrapolate the expected doses during predefined commercial routes. However, their estimations may not be accurate enough. In this work, we present ACORDE (Application COde for the Radiation Dose Estimation), a new framework to estimate the dose onboard flights by exploiting Monte-Carlo capabilities on current HPC and cloud-based facilities. The actual route of any commercial flight is obtained from public trackers and is segmented. The expected secondary flux is calculated along each segment by considering local and real-time atmospheric and geomagnetic conditions. This modulated flux of ionizing radiation is propagated through a Geant4 model of the used aircraft and an anthropomorphic phantom to compute the total dose. The flexibility of ACORDE allows us to calculate not only the actual dose but also other effects such as the impact of course or altitude changes during a particular flight, providing valuable information that could assist in operational decision-making.