Miniaturized three-dimensional (3D) cell culture systems, in particular organoids and spheroids, hold great potential for studying morphogenesis, disease modeling, and drug discovery. However, sub-cellular resolution 3D imaging of these biological samples remains a challenge. Histology, the gold standard for ex vivo microscopic interrogation of tissue anatomy, may address this challenge once the associated techniques are adapted. Due to their small size and delicate structure, organoids must be embedded in a supporting hydrogel. The histological sections have low information content because the distribution of the organoids within the gel is not controlled. To address this issue, we introduce an acoustic micromanipulation platform that concentrates and aligns organoids within a histology-compatible hydrogel block. Utilizing an array of micromachined lead zirconate titanate (PZT) transducers, the platform generates localised and precisely controlled acoustic standing waves to levitate organoids to a prescribed plane and fix their positions within a polyethylene glycol diacrylate (PEGDA)-gelatine hydrogel. Organoids from different culture conditions can be co-embedded in a traceable fashion with the use of a custom-design hydrogel grid. Our results demonstrate that more than 70% of spheroids can be positioned within a 150 μm-thick hydrogel block, substantially increasing the information content of histology sections. The platform's versatility, scalability, and ease of use will make histological assessment accessible to every life science laboratory.