Three-dimensional carbon-based structures have proven useful for tailoring material properties in structural mechanical and energy storage applications. One approach to obtain them has been by carbonization of selected metal-organic frameworks (MOFs) with catalytic metals, but this is not applicable to most common MOF structures. Here, we present a strategy to transform common MOFs, by guest inclusions and high-temperature MOF-guest interactions, into complex carbon-based, diatom-like, hierarchical structures (named for the morphological similarities with the naturally existing diatomaceous species). As an example, we introduce metal salt guests into HKUST-1-type MOFs to generate a family of carbon-based nano-diatoms with two to four levels of structural hierarchy. We report control of the morphology by simple changes in the chemistry of the MOF and guest, with implications for the formation mechanisms. We demonstrate that one of these structures has unique advantages as a fast-charging lithium-ion battery anode. The tunability of composition should enable further studies of reaction mechanisms and result in the growth of a myriad of unprecedented carbon-based structures from the enormous variety of currently available MOF-guest candidates.