Volumetric optoacoustic tomography has been shown to provide unprecedented capabilities for ultrafast imaging of cardiovascular dynamics in mice. Three-dimensional imaging rates in the order of 100 Hz have been achieved, which enabled the visualization of transient cardiac events such as arrhythmias or contrast agent perfusion without the need for retrospective gating. The fast murine heart rates (400–600 beats per minute) yet impose limitations when it comes to compounding of multiple frames or accurate registration of multi-spectral data. Herein, we investigate on the capabilities of Fourier analysis of four-dimensional data for coregistration of independent volumetric optoacoustic image sequences of the heart. The fundamental frequencies and higher harmonics of respiratory and cardiac cycles could clearly be distinguished, which facilitated efficient retrospective gating without additional readings. The performance of the suggested methodology was successfully demonstrated by compounding cardiac images acquired by raster-scanning of a spherical transducer array as well as by unmixing of oxygenated and deoxygenated hemoglobin from multi-spectral optoacoustic data.