Amyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disease characterised by the loss of motor control. Current understanding of ALS pathology is largely based on the post-mortem investigation of advanced disease. A precise in-vivo description of the microstructural changes that characterize early disease stages, and their subsequent development, is therefore lacking. Recent advances in ultra-high field (7T) MRI modelling allow us to investigate microcircuits, such as cortical layers, in-vivo. These automated methods reveal microarchitectural changes in the sub-millimeter range. To apply these methods of in-vivo histology to living ALS-patients, we used sub-millimeter qT1 and QSM data with functional localizers of cortical fields. We precisely characterized the in-vivo pathology in the primary motor cortex (M1) in 12 ALS-patients, in reference to 12 age-, gender-, education- and handedness-matched controls. Longitudinal sampling was performed for a subset of patients. We calculated multimodal pathology maps separately for the superficial layers (layers 2-3), layer 5a, layer 5b and layer 6 of M1 to identify hotspots of demyelination, iron and calcium accumulation in M1, both in behaviorally affected and non-affected cortical fields. Multimodal in-vivo pathology maps reveal critical insights into ALS disease mechanisms. We show that despite layer-specific substance accumulation, the principal layer architecture of M1 is preserved in early disease stages. We identify multiple, small hotspots of pathology within, but also beyond, the first-affected cortical field. In addition, we localize iron accumulation to layer 6, and calcium accumulation to the superficial layer and layer 5a. Longitudinal data show that hotspots of non-topographic calcium accumulation tend to precede demyelination at later time points, where the middle-superficial layers are most affected. These microstructural changes were in accordance with the loss of motor control, as assessed using quantitative behavioral markers of motor function. We show that layer-specific markers of in-vivo pathology can be identified in ALS-patients with a single 7T-MRI measurement after first diagnosis, and that such data provide critical insights into the individual disease state. Our data highlight the non-topographic architecture of ALS disease spread, and the role of calcium rather than iron accumulation in predicting future demyelination. We also highlight a potentially important role of low-myelin borders, that are known to connect to multiple areas within the M1 architecture, in disease spread. Our findings highlight the importance of in-vivo histology for the diagnosis and prognosis of neurodegenerative diseases.