In a 4-year study in a whole-field sanitized organic apple orchard, the effectiveness of nine fungicide treatments, including potassium mono- and bicarbonate and their combinations with wettable sulfur, were evaluated for scab and powdery mildew control on two cultivars with different susceptibility to scab and powdery mildew, under two pruning treatments. The whole-field sanitation practice was performed by removal of infected fallen leaves. Treatment effects on phytotoxicity and yield were also determined. Pruning significantly reduced leaf scab incidence but only on the more scab-susceptible Idared. Pruning significantly reduced mildew incidence in most years and on both cultivars but the more mildew-susceptible Jonathan showed significantly higher mildew incidence than Idared. Among products approved for organic production, the best scab control was achieved with a potassium mono- or bicarbonate treatment combined with wettable sulfur, except for Jonathan in 2011 on leaf and in 2014 on both leaf and fruit, and for Idared in 2013 on fruit. The best mildew control was also achieved with potassium mono- or bicarbonate treatments combined with wettable sulfur, with exceptions on shoots of Idared in 2011 and 2013 and on fruit of Idared in 2012. Leaf phytotoxicity was significantly higher in all potassium carbonate treatments compared with untreated plots, except for Idared in 2012, while fruit russet in these treatments did not differ significantly from the untreated plots. However, phytotoxicity values of all carbonate treatments were significantly lower than the lime sulfur treatment in most years on both cultivars. Yield of the potassium mono- or bicarbonate treatments combined with wettable sulfur was significantly higher than the untreated plots in the pruned treatments for both cultivars in all years. The integrated control approach designed for organic disease management against the two pathogens is discussed.