The Higgs bosons and the top quark decay into rich and diverse final states, containing both light and heavy quarks, gluons, photons as well as W and Z bosons. This article reviews the challenges involved in reconstructing Higgs and top events at the FCC-ee and identifies the areas where novel developments are needed. The precise identification and reconstruction of these final states at the FCC-ee rely on the capability of the detector to provide excellent flavour tagging, jet energy and angular resolution, and global kinematic event reconstruction. Excellent flavour tagging performance requires low-material vertex and tracking detectors, and advanced machine learning techniques as successfully employed in LHC experiments. In addition, the Z pole run will provide abundant samples of heavy flavour partons that can be used for calibration of the tagging algorithms. For the reconstruction of jets, leptons, and missing energy, particle-flow algorithms are crucial to explore the full potential of the highly granular tracking and calorimeter systems, and give access to excellent energy–momentum resolution and precise identification of heavy bosons in their hadronic decays. This enables, among many other key elements, the reconstruction of Higgsstrahlung processes with leptonically and hadronically decaying Z bosons, and an almost background-free identification of top quark pair events. Exploiting the full available kinematic constraints together with exclusive jet clustering algorithms will allow for the optimisation of global event reconstruction with kinematic fitting techniques.