No-tillage is a cropping system that promotes minimal soil disturbance, full residue retention and diverse crop rotation. From a disease perspective, crop rotation is one of the best control measures in no-tillage systems, as many diseases are stubble-borne. A long-term no-tillage systems experiment was conducted from 2007 to 2016 in Western Australia to test effects of crop rotation and residue amount on soil health, crop growth and yield. The current research focusses on the progression of the main stubble-borne and root diseases and plant-parasitic nematodes in this experiment. The research compared a diverse crop rotation with a ‘typical’ farmer rotation, a cereal rotation and wheat monoculture. Three-year rotations were used and the crops and cultivars were changed periodically, within the rotations, to ensure they were relevant to farmers. Levels of root lesion nematode (Pratylenchus neglectus) and Pythium increased most in the pasture and diverse rotations, followed by the wheat monoculture and appeared to decrease slightly in the farmer and cereal rotations. The combination of canola and wheat, along with susceptible chickpea, appeared to favour root lesion nematode. In contrast, fallow and lupin in the farmer rotation appeared most effective at reducing levels. The relatively high numbers of P. neglectus in the pasture was likely due to continuous presence of a number of susceptible weeds and subterranean clover. The crop selections in the diverse rotation of this experiment have generally been a poor choice in terms of P. neglectus, the main nematode threat in Western Australia. By 2016, there was significantly greater Rhizoctonia solani in the soil following cereals compared with canola, chickpea and fallow. Nonetheless, the break crops appeared to have had a relatively short term effect on amounts of R. solani. Over the nine years, Fusarium spp. DNA in the soil increased most in the cereal rotation and wheat monoculture; it hardly changed in the farmer rotation and pasture and it declined in the diverse rotation. There was a decrease in Didymella pinodes/Phoma medicaginis var pinodella DNA (causing pea black spot) in the cereal rotation, farmer rotation and wheat monoculture. In contrast, there was a small increase in pea black spot pathogen DNA in the diverse rotation. This generally reflected the number of pea crops grown, except for the farmer rotation, which had peas grown at the same intensity as the diverse rotation. The difference between these two rotations was likely due to the lower amounts of residue in the farmer rotation, which had fallow and tillage since 2013. As expected, there were higher incidence of the stubble-borne disease in wheat and barley when following the same type of crop. Crop residue management, by windrow burning, had little effect on the level of leaf, root or crown diseases. The differences in host status between crop types and even varieties means that farmers require up-to-date information on the host status if rotations are going to be effective in reducing a broad range of plant-parasitic nematodes and pathogens in soils with no-tillage.