We report on a new enzyme-based method for producing permanently cross-linked pectin microgels. We investigate the shape, size and rheological properties of these microgel particles making comparisons with the more traditional design of calcium cross-linked pectin microgels. Both sets of microgel particles were prepared via the ‘top-down’ mechanical disruption of parent pectin hydrogels. The first hydrogel was prepared from low methoxyl pectin (LMP) (2 wt% pectin) cross-linked using Ca2+ (8.3 mM CaCl2). The LMP microgels show particle sizes ca. 1–100 μm, but are stable only in [Ca2+] = 8.3 mM or above, swelling and/or dissolving rapidly in pure water. The second type of microgel was prepared from sugar beet pectin (SBP) hydrogels covalently cross-linked via laccase. Gelation kinetics were investigated by small amplitude oscillatory shear rheometry. The SBP microgels resisted dissolution in water for several months. Light scattering measurements suggested that the SBP microgel particle sizes were related to the mechanical properties of the parent hydrogels. Various imaging techniques all suggested that SBP microgels have highly irregular shapes, perhaps due to the top-down technique used for their manufacture and their inherent mechanical properties. Concentrating the SBP microgels (to 35–50 wt% microgel, or 0.6–0.8 wt% overall pectin concentration) resulted in suspensions with rheological properties typical of yield stress fluids. When compared at similar overall SBP concentrations, the SBP microgel suspensions offer distinct advantages as bulk rheology modifiers compared to SBP solutions.