Electrochemical discharge machining (ECDM) is an unconventional microfabrication technology which is used for creating microchannels on glass workpieces. Since melting and evaporation are the main mechanisms of material removal in glass workpiece and fabrication of microchannels in ECDM process, the material properties of heat-affected zones (HAZ) would be changed. In this paper, microchannels were machined on soda lime glass in different machining conditions and the nano-indentation test, which is the key tool for identification of changes in material properties of HAZ, was conducted on machined workpieces for measuring the hardness of microchannels’ edges. Experimental results showed that applying a magnetic field in both 15 and 30 wt% electrolyte concentrations leads to an increase in the hardness of the channel edge up to 87 and 24%, respectively. In fact, in the presence of a magnetic field, a magneto-hydrodynamic convention is created, which affects the hydrogen gas bubbles’ movement. So, the electrical conductivity of the solution is enhanced and finally by occurring a more consecutive electrical discharge, a smaller heat-affected zone is created. In addition, due to generation of higher thermal energy, by increasing the electrolyte concentration and applied voltage level, the larger HAZ is created. Analyzing the load-displacement curves of nano-indentation test shows that the hardness of samples machined in the presence of KOH electrolyte is lower than NaOH electrolyte. The potassium ions are larger than sodium ions, leading to a decrease in the sample’s strength and increase in the HAZ. © 2018, Springer-Verlag London Ltd., part of Springer Nature.