Diatomaceous earth are sediments of unicellular algal skeletons with a well-defined hierarchical structure. Despite many tests conducted on systems using diatomaceous earth and epoxy resins, we can find many differences in the methods of acquisition and characteristics of the composite, which may considerably affect the results. In our study, we have conducted tests to verify the impact of the method of obtaining samples and the degassing of the composite on its mechanical properties and standard deviation. The samples were cast in glass moulds and silicone moulds and then subjected to testing for their mechanical and functional properties, imaging with the use of an optical microscope and a scanning electron microscope. The tests have shown that, for samples cast in glass moulds, there is no heterogeneity within the area of the tested sample, as in the case of samples cast in silicone moulds. Silicone moulds allow for quite effective self-degassing of the resin due to the large area-to-mass ratio, and the small remaining air vesicles have a limited effect on the mechanical properties of the samples. The filler used also played a significant role. For systems containing base and rinsed diatomite, it is clear that the degassing of mixtures increases the tensile strength. For treated diatomite, the elongation at break grew along with increasing filler concentration, while for base diatomite, the improvement was observed for flexural strength and impact strength. A non-modified epoxy resin shows a tensile strength at 19.91 MPa (silicone mould cast). At the same time, the degassed, glass mould-cast systems containing 12% of base and rinsed diatoms showed a tensile strength of 27.4 MPa and 44.7 MPa, respectively. We have also observed that the higher the filler concentration, the higher were the tensile strength values, which for the rinsed diatoms reached over 55.1 MPa and for the base diatoms were maximum of 43.8 MPa. The tests, therefore, constitute a set of guidelines and recommendations for testing with the use of fillers showing an extended inner structure.