Over the past decade, the use of magnetic particles (MPs) as labels in magnetic biosensors has attracted increasing interest because it provides a highly sensitive platform that can meet the diagnostic needs that are currently not met by existing technologies. However, preparing magnetic biosensors for a specific diagnostic application is a challenging task, and the (bio)chemical aspects are often neglected. Hence, one of the major remaining bottlenecks in the development of magnetic biosensors is the lack of an optimized magnetosandwich assay for the highly sensitive and specific detection of proteins in complex sample matrices. Therefore, in this article, we report on the impact of several different aspects of magnetosandwich assay development, that is, surface chemistry, MP size, rinsing procedure, sample matrix, and blocking procedure on the total-assay performance using quartz crystal microbalance and optical microscopy analysis. The optimization focused on the diagnostically relevant protein S100betabeta, a marker for stroke and minor head injury. It was observed that small MPs in combination with a strong rinsing and a BSA/Tween-20 blocking allows for the most specific and sensitive detection of S100betabeta in serum over a wide concentration range.