Herbarium specimen digitization and transcription initiatives have led to revitalized use of plant collections making them more accessible than ever. Most digitization is done by producing 2D images of herbarium sheets; however, herbaria also include 3D collections such as fungi, mosses, and dry fruits, among others. Here we present a 3D digitization protocol developed at the Marshall University Herbarium (MUHW) using free photogrammetry software. We tested four freely available software applications, Meshroom, 3DF Zephyr Free, ColMap, and Regard3D on five types of 3D specimens, fungi, a moss, a lichen, a pinecone, and a compound fruit. Using 40–50 images and equipment already available in our herbarium such as a camera and light box, we produced 3D images in less than one hour per specimen. From the four applications tested, 3DF Zephyr Free gave the best results across the different specimens. Specimens that are bilaterally symmetrical or asymmetrical, such as fungi and compound fruit yielded detailed 3D images. Radially symmetrical specimens or specimens with repetitive patterns, such as the pinecone, moss, and lichen, resulted in poor or incomplete 3D images, which indicates that this workflow may be best suited for objects with differentiation in surfaces. Our workflow provides an effective, low-cost method of producing 3D images of 3D herbarium specimens that can be easily implemented in other herbaria.