Alternate bearing pecan trees [Carya illinoinensis (Wangenh.) C. Koch] were hand-thinned annually to 1, ≤2, or ≤3 fruit/cluster or not thinned when the ovule was about one-half expanded. Return bloom was monitored on (1) vegetative shoots, (2) bearing shoots without a second growth flush in the terminal position on 1-year-old branches, (3) bearing shoots without a second growth flush in the lateral position on 1-year-old branches, and (4) bearing shoots with a second growth flush that were primarily in the terminal position. Yield and nut quality were determined in addition to nonstructural carbohydrate, organically bound nitrogen (N), and potassium (K) concentrations in the roots and shoots during January. Fruit thinning improved return bloom but had little effect on weight/nut, kernel percent, or kernel grade. Fruit thinning had either a modest or no effect on nonstructural carbohydrates, organically bound N, and K concentrations. Vegetative shoots and bearing terminal shoots produced a similar number of flowers/1-year-old branch and percentage of flowering current-season shoots. Bearing lateral shoots produced fewer flowers than vegetative shoots most years and fewer flowering current-season shoots during one year. Shoots with a second growth flush produced more flowers/1-year-old branch and a larger percentage of flowering current-season shoots than did vegetative shoots 2 of 3 years. These data indicate fruit thinning of overloaded trees improved return bloom, but the lack of interactions between thinning treatment and shoot type suggests that the number of fruit/cluster was less important than total crop load in determining nut quality and return bloom. Thus removal of entire fruit clusters appears as effective as thinning fruit within a cluster to maintain adequate nut quality and promote return bloom. Nonstructural carbohydrates, organically bound N, and K were not limiting factors in bearing consistency because they were not depressed in unthinned trees. Nonstructural carbohydrates, organically bound N, and K concentrations were not closely linked to alternate bearing because return bloom was enhanced by thinning, but thinning did not affect their concentrations.