Cobalt orthogermanate (GeCo2O4) is a unique system in the family of cobalt spinels ACo2O4 (A= Sn, Ti, Ru, Mn, Al, Zn, Fe, etc.) in which magnetic Co ions stabilize on the pyrochlore lattice exhibiting a large degree of orbital frustration. Due to the complexity of the low-temperature antiferromagnetic (AFM) ordering and long-range magnetic exchange interactions, the lattice dynamics and magnetic structure of GeCo2O4 spinel has remained puzzling. To address this issue, here we present theoretical and experimental investigations of the highly frustrated magnetic structure, and the infrared (IR) and Raman-active phonon modes in the spinel GeCo2O4, which exhibits an AFM ordering below the Néel temperature T N ∼21 K, followed by a cubic (F d 3m) to tetragonal (I41/amd) structural phase transition at T S ∼16 K. Our density-functional theory (DFT+U) calculations reveal that one needs to consider magnetic-exchange interactions up to the third nearest neighbors to get an accurate description of the low-temperature AFM order in GeCo2O4. At room temperature three distinct IR-active modes (T 1u) are observed at frequencies 680, 413, and 325 cm −1 along with four Raman-active modes A1g, T 2g(1), T 2g(2), and E g at frequencies 760, 647, 550, and 308 cm −1 , respectively, which match reasonably well with our DFT+U calculated values. All the IR-active and Raman-active phonon modes exhibit signatures of moderate spin-phonon coupling. The temperature dependence of various parameters, such as the shift, width, and intensity, of the Raman-active modes, is also discussed. Noticeable changes around T N and T S are observed in the Raman line parameters of the E g and T 2g modes, which are associated with the modulation of the Co-O bonds in CoO6 octahedra during the excitations of these modes.