Since 2018, the Belle II experiment has been running at KEK, at the SuperKEKB B-factory, with all detector subsystems taking data. One of the important detector systems is an electromagnetic calorimeter (ECL) that includes 8736 counters based on CsI(Tl) scintillation crystals. This report describes the data acquisition (DAQ) system that has been developed for ECL. Front-end electronics of ECL DAQ consist of several hundred highly configurable FPGA-controlled modules that utilize pipeline readout architecture and are able to handle a trigger rate up to 30 kHz. ECL front end electronics are initialized, configured and monitored by ECL DAQ software. The initialization library can work with several transport protocols, internally optimize requests to the electronics and perform caching of the configuration data. Configuration software manages and monitors more than 105 electronics parameters and updates them based on the calibrations. Continuous monitoring of ECL data quality is also implemented.