Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms: a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). We previously used an in vitro supported-lipid bilayer reconstitution system to show that stoichiometric levels of the processed, short form of Opa1 (s-Opa1) work together with l-Opa1 to mediate efficient and fast membrane pore opening (Ge et al., eLife 2020). Our understanding of the mechanisms for how Opa1 form influences cristae shape has remained less well defined. We performed in situ cryo-electron tomography of cryo-focused ion beam milled mammalian cells with well-defined Opa1 states to understand how each form of Opa1 influences cristae architecture. We describe differences in cristae geometry, membrane spacings, and subcompartment volumes. We find the absence of l-Opa1 results in mitochondria with wider cristae junctions and cells less sensitive to apoptotic stimuli, implicating l-Opa1 mediating the cytochrome c release process via the cristae junction. We discuss the implications Opa1-dependent ultrastructure in organelle function.