To develop efficient solid-state photosynthetic cell factories for sustainable chemical production, we present an interdisciplinary experimental toolbox to investigate and interlink the structure, operative stability, and gas transfer properties of alginate- and nanocellulose-based hydrogel matrices with entrapped wild-type Synechocystis PCC 6803 cyanobacteria. We created a rheological map based on the mechanical performance of the hydrogel matrices. The results highlighted the importance of Ca2+-cross-linking and showed that nanocellulose matrices possess higher yield properties, and alginate matrices possess higher rest properties. We observed higher porosity for nanocellulose-based matrices in a water-swollen state via calorimetric thermoporosimetry and scanning electron microscopy imaging. Finally, by pioneering a gas flux analysis via membrane-inlet mass spectrometry for entrapped cells, we observed that the porosity and rigidity of the matrices are connected to their gas exchange rates over time. Overall, these findings link the dynamic properties of the life-sustaining matrix to the performance of the immobilized cells in tailored solid-state photosynthetic cell factories.