Most apple cultivars produce too many flowers to enable consistent yields of high-quality fruit, thus, crop load management (thinning) is an integral part of orchard management in modern apple cultivation. Crop load is managed by thinning excess flowers and/or fruit from a tree, however ideal targets vary between cultivars. In this two-year study, the effect of thinning methods at different levels of crop load on fruit quality and production, post-harvest storability and physiological disorders, and fruit and leaf nutrient content in ‘Scilate’ apples were investigated in southern Tasmania, Australia. Two thinning methods, artificial bud extinction (ABE) and hand thinning (HT), were compared at three levels of crop load: 3, 6, or 12 fruit cm−2 limb cross-sectional area (LCSA), described as low, medium, and high, respectively. During the second season, all the ABE and HT treatments received additional chemical thinning (CT). The results demonstrated that ABE consistently outperformed HT in terms of improved fruit set, return bloom, and fruit weight. The fruit quality parameters, such as flesh firmness, total soluble solids, dry matter content, malic acid content, and fruit shape, were also improved under the ABE regime, with these positive effects being the clearest in the second season. In general, high-quality fruits were obtained from the low and medium crop loads, while the fruit quality was poor for the high crop load trees, but the low crop load fruit had a slightly higher incidence of internal flesh browning (predominantly radial) and fruit softening after regular atmosphere storage. The crop load also impacted on the fruit and leaf mineral nutrient content, where fruit N, Ca, Mn, and Zn, and leaf N, Fe, Zn, and Cu content increased while fruit and leaf K declined with a higher crop load. High crop load, irrespective of the thinning regime, and HT with a medium crop load, induced severe biennial bearing, whereas, the fruit yield was relatively consistent with ABE, even with a medium crop load. We conclude that ABE with a medium crop load (around six fruit cm−2 LCSA) is an effective method of managing crop load and optimizing the fruit quality in ‘Scilate’ apples.