Phytophthora root rot, caused by Phytophthora cactorum, is an economically important disease on young apple trees. Limited information is available on the effect of different phosphonate application methods and dosages on disease control, fruit- and root phosphite concentrations and soil- and root pathogen inoculum levels. Evaluation of phosphonate treatments in three apple orchard trials (two in the Grabouw and one in the Koue Bokkeveld region) showed that foliar sprays (ammonium- or potassium phosphonate), trunk sprays and trunk paints, were equally effective at increasing trunk diameter in one trial and yield in a second trial over a 25-month period. Foliar ammonium- and potassium phosphonate sprays (12 g phosphorous acid/tree), and two different dosages of the ammonium phosphonate sprays (~ 4.8 g or 12 g phosphorous acid/tree) were all equally effective at improving tree growth. The addition of a bark penetrant (polyether-polymethylsiloxane-copolymer) to trunk sprays did not improve the activity of trunk sprays. The low dosage ammonium phosphonate foliar spray (~4.8 g a.i./tree) was the only treatment that in general yielded significantly lower root phosphite concentrations than the other phosphonate treatments. Root phosphite concentrations were significantly positively correlated (P < 0.0001) with an increase in trunk diameter and negatively with P. cactorum root DNA quantities (P ≤ 0.001). Phosphite fruit residues were less than 31 ppm for all treatments, with the trunk paint treatment (80 g phosphorous acid/tree applied annually) yielding significantly lower residues than the higher dosage foliar sprays (~12 g a.i/tree). Twenty-one months post-treatment, most of the phosphonate treatments in all of the trials similarly significantly reduced P. cactorum DNA quantities estimated directly from roots, but not from soil based on soil baiting DNA analysis. Pathogen quantities in fine feeder roots did not differ significantly from those in higher-order roots (< 5 mm dia.). Phytophthora cactorum DNA quantities estimated using DNA quantification directly from roots were significantly correlated (P < 0.0001) with those obtained through root leaf baiting DNA analysis, and to a lesser extent with soil leaf baiting DNA quantities (P = 0.025).