This deposit contains an open-source workflow for automated counting of germinated and non-germinated conidia of entomopathogenic fungi (e.g., Beauveria bassiana) from microscopy images. It is the supplementary material of the article "Automated Conidial Germination Counter: An Open‑Source Workflow for Entomopathogenic Fungi Quality Control" (Frontiers in Fungal Biology). Contents: Three Fiji/ImageJ macros: batch preprocessing, manual counting assistant, and fully automated conidial germination counter. A pre‑trained ilastik pixel classifier (project file + 5 training images). 10 raw demo images for testing. Requirements: Fiji (Fiji Is Just ImageJ) ilastik 1.4.0 or newer Quick start: Open the ilastik project (classifier.ilp) and export probability maps for your images (TIFF, multi‑channel). Run the Batch_Conidial_Germination_Automated_Counter.ijm macro in Fiji on the exported maps. Obtain germination percentages and visual audit images (overlaid contours). The workflow achieves 97% concordance with manual counting, processes each image in ~10 seconds, and performs a full census (3,000–9,000 conidia per sample). All material is released under BSD 2‑Clause license. See the README.txt inside the ZIP for detailed step‑by‑step instructions.