Experimental data of the manuscript "Mycobacterium detection method combining filtration, immunomagnetic separation, and electrochemical readout in a portable biosensing device", published in Sensors and Actuators B: Chemical, https://doi.org/10.1016/j.snb.2023.135211. This study addresses a straightforward and highly sensitive approach for detecting Mycobacterium fortuitum. The method involves a combination of filtration and direct immunomagnetic separation to isolate the bacteria retained on filters for further electrochemical magneto immunosensing in a handheld device. Unlike conventional methods involving pre-enrichment by culturing, this approach employs a simplified preconcentration technique, which includes filtration of large water samples, up to 100 mL, followed by a one-step process of immunomagnetic separation and labeling. After a 60-min, during which the filter with the retained bacteria and all the reagents (including modified magnetic particles and enzymatic conjugates) are incubated, the resulting product is directly drop into a cartridge, capable of performing magnetic actuation and washing. The electrochemical readout is carried out on a portable battery operated device within 30 sec. Remarkably, the immunosensor demonstrates an outstanding limit of detection of 5 CFU mL-1 in hemodialysis water processing 100 mL of sample. This achievement is remarkable considering the short and simplified analytical procedure, compared to the traditional isolation and culturing of mycobacteria, which typically takes 2 weeks.