Herein, we synthesize 3D nanoflower-like MCo₂O₄@MCo₂S₄@polypyrrole (M = Cu, Mn) core–shell composites on nickel foam (NF). CuCo₂O₄ (CuC) and MnCo₂O₄ (MnC) nanowires and CuCo₂S₄ (CuS) and MnCo₂S₄ (MnS) nanosheets grow vertically on NF as the core by hydrothermal and calcination methods and a PPy film covered on the surface of MCo₂O₄@MCo₂S₄ (M = Cu, Mn) as the shell via a chemical bath method to form 3D self-supporting nanoflower-like composite materials. The as-prepared MC@MS@PPy-16/NF (M = Cu, Mn) electrode materials are characterized by field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). Due to the particularity of the electrode material structure, the MC@MS@PPy-16 (M = Cu, Mn) electrode has a high specific capacitance (C_s, 413.63 mA h g⁻¹ and 654.64 mA h g⁻¹ at 1 A g⁻¹) and the C_s retention rate exceeds 90% after 10 000 cycles. The asymmetric supercapacitor (ASC) device assembled with the MC@MS@PPy-16 (M = Cu, Mn) electrode as the positive electrode, active carbon (AC) as the negative electrode and 6 M KOH as the electrolyte can work stably in a broad voltage range of 0–1.6 V. MC@MS@PPy-16//AC ASC (M = Cu, Mn) devices display excellent electrical characteristics in terms of high energy density (41.34 and 38.75 W h kg⁻¹ at 8000 W kg⁻¹) and cycling stability (C_s retention rates of 84.74% and 80.4% and coulombic efficiencies of 80.15% and 83.69%). These results show that MCo₂O₄@MCo₂S₄@polypyrrole composite materials have great application potential in high-performance supercapacitors.