The main purpose of this experiment was to develop a multifunctional nutraceutical composition based on ingredients of different origins (Spirulina powder (SP), bovine colostrum (BC), Jerusalem artichoke powder (JAP), and apple cider vinegar (ACV)) which possess different health benefits through their different mechanisms of action. In order to improve the functional properties of Spirulina and bovine colostrum, fermentation with the Pediococcus acidilactici No. 29 and Lacticaseibacillus paracasei LUHS244 strains, respectively, was carried out. These LAB strains were chosen due to their good antimicrobial properties. The following parameters were analysed: for Spirulina (non-treated and fermented)—pH, colour coordinates, fatty acid profile, and contents of L-glutamic and GABA acids; for bovine colostrum (non-treated and fermented)—pH, colour coordinates, dry matter, and microbiological parameters (total LAB, total bacteria, total enterobacteria, Escherichia coli, and mould/yeast counts); for the produced nutraceuticals—hardness, colour coordinates, and overall acceptability. It was established that fermentation reduced the pH of the SP and BC and affected their colour coordinates. Fermented SP contained a greater concentration of gamma-aminobutyric and L-glutamic acids (by 5.2 times and 31.4% more, respectively), compared to the non-treated SP and BC. In addition, the presence of gamma-linolenic and omega-3 fatty acids was observed in fermented SP. Fermentation of BC reduces Escherichia coli, total bacteria, total enterobacteria, and total mould/yeast counts in samples. The obtained three-layer nutraceutical (I layer—fermented SP; II—fermented BC and JAP; III—ACV) demonstrated a high overall acceptability. Finally, our finding suggest that the selected nutraceutical combination has immense potential in the production of a multifunctional product with improved functionality and a high acceptability.