The Automated and Integrated Seafloor Classification Workflow (AI-SCW) is a semi-automated underwater image processing pipeline that has been customized for use in classifying the seafloor into semantic habitat categories. The current implementation has been tested against a sequence of underwater images collected by the Ocean Floor Observation System (OFOS), in the Clarion-Clipperton Zone of the Pacific Ocean. Despite this, the workflow could also be applied to images acquired by other platforms such as an Autonomous Underwater Vehicle (AUV), or Remotely Operated Vehicle (ROV). The modules in AI-SCW have been implemented using the python programming language, specifically using libraries such as scikit-image for image processing, scikit-learn for machine learning and dimensionality reduction, keras for computer vision with deep learning, and matplotlib for generating visualizations. Therefore, AI-SCW modularized implementation allows users to accomplish a variety of underwater computer vision tasks, which include: detecting laser points from the underwater images for use in scale determination; performing contrast enhancement and color normalization to improve the visual quality of the images; semi-automated generation of annotations to be used downstream during supervised classification; training a convolutional neural network (Inception v3) using the generated annotations to semantically classify each image into one of pre-defined seafloor habitat categories; evaluating sampling strategies for generation of balanced training images to be used for fitting an unsupervised k-means classifier; and visualization of classification results in both feature space view and in map view geospatial co-ordinates. Thus, the workflow is useful for a quick but objective generation of image-based seafloor habitat maps to support monitoring of remote benthic ecosystems.