In this study, the citrate–nitrate auto combustion process was used to create spinel ferrite nanoparticles Mn0.5Cu0.5ErxFe2−xO4, where 0.0 ≤ x ≤ 0.075. An analysis was conducted to evaluate the influence of erbium doping on the antimicrobial, microstructural, morphological, and magnetic possessions. A pure single-phase cubic structure is revealed by the structural study of the produced samples with Er doping, but the second phase emerges at x = 0.075. Results show that the lattice parameter grows with incorporating Er3+ concentration up to x = 0.06, after which it starts to drop at x = 0.075, which lies between 8.432 and 8.446 Å. The TEM pictures revealed nanoscale dimensions and a cubic spinel structure. A rise in the Er3+ content in Mn-Cu nanoferrites caused a dramatic variation in the magnetic properties. The coercivity varied from 93.60 to 114.89 G, whereas the saturation magnetization (ranging from 54.83 to 40.42 emu/g) and remanence (from 11.57 to 7.61 emu/g) showed a general decreasing trend. The results of the microwave frequency measurements show that ferrites can be used in wireless communication technology. The evaluation of the antimicrobial efficacy of MCEF nanoparticles against pathogenic microorganisms, including Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, Fusarium oxysporum, Aspergillus flavus, A. terreus, A. fumigatus, A. niger, and Rhizopus sp., demonstrated that MCF nanoparticles doped with erbium at concentrations of 0.03 and 0.075 exhibit enhanced inhibitory effects on the growth of all aforementioned microorganisms. The highest inhibition was observed at an erbium concentration of 0.075, with a mean crystallite size of 39.16 nm, surpassing the inhibition at 0.03 concentration, which had an average size of 49.36 nm, in comparison to the undoped nanoparticles. The microbiological studies demonstrate that these nanoparticles may serve as a prospective antimicrobial agent with reduced effects on P. aeruginosa.