Quantum entanglement has been identified as a crucial concept underlying many intriguing phenomena in condensed matter systems, such as topological phases or many-body localization. Recently, instead of considering mere quantifiers of entanglement such as entanglement entropy, the study of entanglement structure in terms of the entanglement spectrum has shifted to a focus leading to new insights into fractional quantum Hall states and topological insulators, among others. What remains a challenge is the experimental detection of such fine-grained properties of quantum systems. The development of protocols for detecting features of the entanglement spectrum in cold-atom systems, which are one of the leading platforms for quantum simulation, is thus highly desirable and will open up new avenues for experimentally exploring quantum many-body physics. Here, we present a method to bound the width of the entanglement spectrum, or entanglement dimension, of cold atoms in lattice geometries, requiring only measurements in two experimentally accessible bases and utilizing ballistic time-of-flight (TOF) expansion. Building on previous proposals for entanglement certification for photon pairs, we first consider entanglement between two atoms of different atomic species and later generalize to higher numbers of atoms per species and multispecies configurations showing multipartite high-dimensional entanglement. Through numerical simulations, we show that our method is robust against typical experimental noise effects and thus will enable high-dimensional entanglement certification in systems of up to eight atoms using currently available experimental techniques.