Photogrammetry is rapidly emerging as the preeminent tool for quantifying benthic marine communities. Photogrammetry pipelines have strong potential for widespread application in benthic marine monitoring due to low financial and technical in-field inputs required to generate a diversity of high-resolution 2D and 3D habitat data. Despite the widespread use of underwater photogrammetry, important user inputs during data collection and model processing are often unreported and potentially overlooked. These inputs can have significant implications for the comparability of datasets and are essential considerations during the design and implementation of photogrammetry-based monitoring programs. Here we present a detailed, rigorously field-tested protocol for monitoring benthic communities using time-series photogrammetry data at spatial scales of 70 – 1500 square meters and output pixel resolutions of 0.3 – 5 mm. Vital learnings and considerations of key stages of this pipeline are examined, from in-water techniques to final output generation. We also examine how this workflow has been successfully implemented in one of the largest photogrammetry-based reef monitoring programs in Australia, spanning >350 reef sites from the Torres Strait to the Southern GBR. Lastly, we discuss future opportunities provided by these workflows and how these may be altered to suit a variety of applications and stakeholders.