This paper addresses a comparative study of immunomagnetic separation of Salmonella using micro and nano-sized magnetic carriers. In this approach, nano (300nm) and micro (2.8μm) sized magnetic particles were modified with anti-Salmonella antibody to pre-concentrate the bacteria from the samples throughout an immunological reaction. The performance of the immunomagnetic separation on the different magnetic carriers was evaluated using classical culturing, confocal and scanning electron microscopy to study the binding pattern, as well as a magneto-actuated immunosensor with electrochemical read-out for the rapid detection of the bacteria in spiked milk samples. In this approach, a second polyclonal antibody labeled with peroxidase as electrochemical reporter was used. The magneto-actuated electrochemical immunosensor was able to clearly distinguish between food pathogenic bacteria such as Salmonella enterica and Escherichia coli, showing a limit of detection (LOD) as low as 538CFUmL−1 and 291CFUmL−1 for magnetic micro and nanocarriers, respectively, in whole milk, although magnetic nanoparticles showed a noticeable higher matrix effect and higher agglomeration effect. These LODs were achieved in a total assay time of 1h without any previous culturing pre-enrichment step. If the samples were pre-enriched for 8h, the magneto immunosensor based on the magnetic nanoparticles was able to detect as low as 1CFU in 25mL of milk (0.04CFUmL−1).