Climate change is increasingly affecting the nutritional content and structural integrity of horticultural crops, leading to challenges such as diminished fruit quality and the exacerbation of fruit cracking. This manuscript systematically explores the multifaceted impacts of these changes, with a particular focus on the nutritional quality and increased incidence of fruit cracking. An exhaustive review of current research identifies the critical role of transcription factors in mediating plant responses to climatic stressors, such as drought, temperature extremes, and saline conditions. The significance of transcription factors, including bHLH, bZIP, DOF, MDP, HD-ZIP, MYB, and ERF4, is highlighted in the development of fruit cracking, underscoring the genetic underpinnings behind stress-related phenotypic outcomes. The effectiveness of greenhouse structures in mitigating adverse climatic effects is evaluated, offering a strategic approach to sustain crop productivity amidst CO2 fluctuations and water scarcity, which are shown to influence plant physiology and lead to changes in fruit development, nutrient dynamics, and a heightened risk of cracking. Moreover, the manuscript delves into advanced breeding strategies and genetic engineering techniques, such as genome editing, to enhance crop resilience against climatic challenges. It also discusses adaptation strategies vital for sustainable horticulture, emphasizing the need to integrate novel genetic insights with controlled environment horticulture to counteract climate change's detrimental effects. The synthesis presented here underscores the urgent need for innovative breeding strategies aimed at developing resilient crop varieties that can withstand climatic uncertainty while preserving nutritional integrity.