School gardens have become common school-based health promotion strategies to enhance dietary behaviors in the United States. The goal of this study was to examine the effects of TX Sprouts, a one-year school-based gardening, cooking, and nutrition cluster randomized controlled trial, on students dietary intake and quality. Eight schools were randomly assigned to the TX Sprouts intervention and eight schools to control (i.e., delayed intervention) over three years (2016-2019). The intervention arm received: formation and training of Garden Leadership Committees; a 0.25-acre outdoor teaching garden; 18 student lessons including gardening, nutrition, and cooking activities, taught weekly in the teaching garden during school hours; and nine parent lessons, taught monthly. Dietary intake data via two 24 h dietary recalls (24 hDR) were collected on a random subsample (n = 468). Dietary quality was calculated using the Healthy Eating Index 2015 (HEI-2015). The intervention group compared to control resulted in a modest increase in protein intake as a percentage of total energy (0.4% vs. -0.3%, p = 0.021) and in HEI-2015 total vegetables component scores (+4% vs. -2%, p = 0.003). When stratified by ethnicity/race, non-Hispanic children had a significant increase in HEI-2015 total vegetable scores in the intervention group compared to the control group (+4% vs. -8%, p = 0.026). Both the intervention and control groups increased added sugar intake; however, to a lesser extent within the intervention group (0.3 vs. 2.6 g/day, p = 0.050). School-based gardening, cooking, and nutrition interventions can result in significant improvements in dietary intake. Further research on ways to scale and sustain nutrition education programs in schools is warranted. The trial is registered at ClinicalTrials.gov (NCT02668744).