The effectiveness of predictive microbiology is limited by the lack of knowledge concerning the influence of food microstructure on microbial dynamics. Therefore, future modelling attempts should be based on experiments in structured food model systems as well as liquid systems. In this study, fish-based model systems with various microstructures were developed, i.e., two liquid systems (with and without xanthan gum), an emulsion, an aqueous gel, and a gelled emulsion. The microstructural effect was isolated by minimising compositional and physico-chemical changes among the different model systems. The systems were suitable for common growth and mild thermal inactivation experiments involving both homogeneous and surface inoculation. Average pH of the model systems was 6.36 ± 0.03 and average aw was 0.988 ± 0.002. The liquid system without xanthan gum behaved like a Newtonian fluid, while the emulsion and the liquid containing xanthan gum exhibited (non-Newtonian) pseudo-plastic behaviour. Both the aqueous gel and gelled emulsion were classified as strong gels, with a hardness of 1.35 ± 0.07 N and 1.25 ± 0.05 N, respectively. Fat droplet size of the emulsion and gelled emulsion model systems was evenly distributed around 1 μm. In general, the set of model systems was proven to be suitable to study the influence of important aspects of food microstructure on microbial dynamics.