The Data Acquisition (DAQ) system of the J-PARC KOTO experiment has recently undergone a major upgrade, increasing its throughput and adding sophisticated event selection at the High Level Trigger (HLT). This upgrade is motivated by an ongoing beam intensity upgrade at the accelerator, by the need of more data to improve the precision of data-driven measurements involved in the $K_L \to \pi^0 \nu \overline{\nu}$ search, and to leave enough room for alternative physics searches, such as the $K_L \to \pi^0 e^+ e^-$ decay. The upgraded DAQ system performs event building on FPGAs, and includes a new HLT where event reconstruction, selection, and data compression are performed on GPUs. The main features of the DAQ system, focusing on the High Level Trigger, are presented.