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Abstract EX Lupi, a low-mass young stellar object, went into an accretion-driven outburst in 2022 March. The outburst caused a sudden phase change of ∼112° ± 5° in periodically oscillating multiband lightcurves. Our high-resolution spectra obtained with the High Resolution Spectrograph (HRS) on board the Southern African Large Telescope also revealed a consistent phase change in the periodically varying radial velocities (RVs), along with an increase in the RV amplitude of various emission lines. The phase change and increase in RV amplitude morphologically translates to a change in the azimuthal and latitudinal location of the accretion hotspot over the stellar surface, which indicates a reconfiguration of the accretion funnel geometry. Our three-dimensional magnetohydrodynamic simulations reproduce the phase change for EX Lupi. To explain the observations, we explored the possibility of forward shifting of the dipolar accretion funnel as well as the possibility of the emergence of a new accretion funnel. During the outburst, we also found evidence of the hotspot’s morphology extending azimuthally asymmetrically with a leading hot edge and cold tail along the stellar rotation. Further, our high-cadence photometry showed that the accretion flow has clumps. We also detected possible clumpy accretion events in the HRS spectra that showed episodically highly blueshifted wings in the CaiiIR triplet and Balmer H lines.