Precise indoor microclimate control in greenhouses is essential for optimizing crop growth, productivity, and thermal stability throughout the year. Temperature and humidity regulation directly affect plant physiology, photosynthesis, and yield quality, positioning environmental control as a central component of modern protected agriculture. In this context, shallow geothermal systems and geothermal heat pumps have emerged as efficient solutions for continuous heating and cooling, leveraging the soil’s thermal inertia to stabilize internal conditions and reduce dependence on external climatic variability. This study analyzes the scientific and technical evolution of geothermal energy applications in protected agriculture through a bibliometric and conceptual approach. A structured TITLE-ABS-KEY search equation was applied to international databases, integrating terms related to geothermal energy, heat pumps, greenhouses, and microclimatic variables, while excluding studies focused primarily on emissions or large-scale environmental assessments. The resulting dataset comprises 103 documents published between 2016 and 2025, distributed across 78 sources and involving 423 authors. Keyword co-occurrence and thematic mapping reveal that “greenhouses,” “geothermal heat pumps,” and “pumps” function as motor themes, characterized by high centrality and density, indicating their leading role in the research field. In contrast, “geothermal energy,” “geothermal fields,” and “heat transfer” are identified as foundational themes supporting the conceptual structure. Emerging topics such as precise indoor temperature control, air distribution, detailed numerical simulation, and real-time monitoring show lower levels of development, highlighting critical research gaps. The results demonstrate a transition from descriptive studies toward advanced modeling approaches, including numerical simulations and coupled soil–structure–air systems aimed at improving thermal uniformity and system efficiency. It is concluded that integrating multiphysics modeling with intelligent control strategies represents the main opportunity for enhancing the design, scalability, and operational performance of geothermal systems in greenhouse environments.