The stabilizing capacity of crystalline inulin during spray-drying and storage of Lactobacillus plantarum CIDCA 83114 was assessed. In a first step, the physical properties of the matrices were investigated, using amorphous inulin as control. Melting and glass transition temperatures, water sorption isotherms, water activity, and infrared spectra were determined. Microorganisms were spray-dried at a pilot scale in both amorphous and crystalline matrices. After that, scanning electronic and confocal microsopies provided a full landscape about the interactions between microorganisms and crystals, and also the bacterial location within the amorphous matrices. The technological properties of the dehydrated microorganisms (culturability and acidification capacity) during storage at different water activities were also evaluated. Both amorphous and crystalline inulins were adequate matrices to stabilize microorganisms. However, crystalline inulin was more stable than amorphous one, especially when the storage temperature was close to the glass transition temperature, resulting in a better matrix to protect microorganisms during pilot spray-drying and storage. Furthermore, no accumulation of insoluble inulin was observed after resuspending the dehydrated microorganisms in crystalline inulin matrices, which appears as a clear technological advantage with regard to the amorphous one. Considering the prebiotic character of inulin and the probiotic properties of L. plantarum CIDCA 83114, this work developed an integrated approach, both from a fundamental and from an applied viewpoint, supporting the incorporation of such ingredients in the formulation of food products.