This review provides an overview of the current methods for quantifying mitochondrial ultrastructure, including cristae morphology, mitochondrial contact sites, and recycling machinery and a guide to utilizing electron microscopy to effectively measure these organelles. Quantitative analysis of mitochondrial ultrastructure is essential for understanding mitochondrial biology and developing therapeutic strategies for mitochondrial-related diseases. Techniques such as transmission electron microscopy (TEM) and serial block face-scanning electron microscopy, as well as how they can be combined with other techniques including confocal microscopy, super-resolution microscopy, and correlative light and electron microscopy are discussed. Beyond their limitations and challenges, we also offer specific magnifications that may be best suited for TEM analysis of mitochondrial, endoplasmic reticulum, and recycling machinery. Finally, perspectives on future quantification methods are offered. •Suggestions for transmission electron microscopy measurement of mitochondria, their contact sites, and recycling machinery.•Measurement techniques for mitochondria, their contact sites, recycling machinery, endoplasmic reticulum, and Golgi Apparatus.•Critique of the current literature regarding TEM quantification and considerations for future 3D analysis.•TEM from our laboratory across a range of tissues demonstrating the functional impact of these literature-backed suggestions.