Cosmological observations as well as theoretical approaches to physics beyond the standard model provide strong motivations for experimental tests of fundamental symmetries, such as CPT invariance. In this context, the availability of cold baryonic antimatter at CERN has opened an avenue for ultrahigh-precision comparisons of protons and antiprotons in Penning traps. This work discusses an experimental method inspired by quantum logic techniques that will improve particle localization and readout speed in such experiments. The method allows for sympathetic cooling of the (anti-)proton to its quantum-mechanical ground state as well as the readout of its spin alignment, replacing the commonly used continuous Stern–Gerlach effect. Both of these features are achieved through coupling to a laser-cooled 'logic' ion co-trapped in a double-well potential. This technique will boost the measurement sampling rate and will thus provide results with lower statistical uncertainty, contributing to stringent searches for time dependent variations in the data. Such measurements ultimately yield extremely high sensitivities to CPT violating coefficients acting on baryons in the standard-model extension, will allow the exploration of previously unmeasured types of symmetry violations, and will enable antimatter-based axion-like dark matter searches with improved mass resolution.