The present work reported the synthesis of pure Co₃O₄ and Cu–Co₃O₄ nanocrystals by the PEG (polyethylene glycol)-assisted microwave heating route. The crystallinity, morphology, elemental composition, and optical and electrical properties of the as-synthesized materials were characterized by XRD, FE-SEM, EDX, FTIR, UV-vis, PL, BET, EIS, and CV (electrochemical behavior) studies. The existence of cubic nanocrystals with interstitial doping was confirmed by XRD analysis. The incorporation of the dopant resulted in a reduction in the crystallite size of the synthesized samples. In addition, crystallite sizes were calculated from XRD peak broadening using both Scherrer and William–Hall plot methods. The crystallinity of the samples was confirmed by FESEM images and EDX analysis of elemental composition revealed the presence of dopant elements in the synthesized sample. FTIR spectra indicated the two absorption bands from the stretching vibration of the metal–oxygen bonds in Co₃O_4. The optical properties of Cu–Co₃O₄ nanocrystals examined using UV-visible spectroscopy showed a shift of maximum absorption to the UV region (blue shift), indicating an increase in band-gap energy. Photoluminescence spectroscopy was used to measure the trapping efficiency and migration of charge carriers which revealed the electron–hole pair's recombination behavior. The specific surface area of the synthesized samples was recorded by BET analysis. Electrochemical measurements were performed on modification of the glassy carbon electrode (GCE) with multi-walled carbon nanotubes (MWCNT) decorated with Co₃O₄ and Cu–Co₃O₄ using cyclic voltammetry and electrochemical impedance studies. The photocatalytic performance of both pure and Cu–Co₃O₄ nanocrystals was evaluated by the degradation of EY dye under UV-visible light irradiation. Experimental parameters including the initial dye concentration, catalyst dose, and pH were ascertained under favorable conditions for photocatalytic degradation. The maximum degradation (84.50%) was achieved at natural pH for continuous irradiation up to 300 min. The experimental results showed that the incorporation of Cu into pure Co₃O₄ enhanced its photocatalytic activity, which is due to a decreased rate of electron–hole recombination and an increase in specific surface area of Cu–Co₃O₄ nanocrystals. The in situ capture study suggests that the major active species were found to be photogenerated holes (h⁺) and superoxide radical anions (˙O₂⁻) for the degradation of EY dye. The predicted masses of fragments are well justified by the mass spectral data and the cycling degradation of EY showed good reusability for Cu–Co₃O₄. The antimicrobial activity of pure Co₃O₄ and Cu–Co₃O₄ nanocrystals was investigated using the well-diffusion method against Gram-negative (Streptococcus mutans) and Gram-positive (Salmonella typhi) bacterial strains. Cu–Co₃O₄ nanocrystals can be a good candidate for environmental remediation.