Two sol-gel materials based on tetraethylorthosilicate (TEOS) and a combination of methacryloxypropyltrimethoxysilane and zirconium propoxide were developed and used as host matrices for the organic catalyst (l-proline) and iron oxide nanoparticles with the objective of formulating a magnetic sol-gel catalyst. In order to investigate the effect of the sol-gel condensation process on the catalyst recyclability and the effect of the dopants on the structure of the sol-gel matrices, iron oxide nanoparticles and l-proline were introduced in the sol-gel matrices either during the sol-gel synthesis or at the end of the sol-gel synthesis. While both systems were successfully recycled three times when applied to the Aldol reaction, the TEOS based sol-gel material with the dopants introduced at the end of the sol-gel synthesis showed excellent reaction efficiency and recyclability with 99% conversion. In parallel, the zirconium sol-gel-based material did not enable any conversion. Remarkably, it is demonstrated that the process of introducing the dopants strongly effects the condensation of the inorganic networks of the sol-gel matrix by involving the organic catalyst in the catalysis of the condensation of the inorganic moieties. Furthermore, this condensation process is shown to play a major role in the mobility of the organic catalyst and therefore on its ability to be recycled. This study is, to our knowledge, the first that investigates the effect of the morphology and structure of sol-gel matrices on the catalytic performance of an organic catalyst.