The present paper aims to quantify the carbon emissions associated with the establishment of 15 walnut orchards (“Juglans californica”) in the greater area of Magnisia, Greece, with the use of a carbon footprint tool interconnected to a Farm Management Information System. The data collection spanned the first five years following the planting of the trees, providing a comprehensive view of the emissions during this critical establishment phase. Over the five-year period examined (February 2019–December 2023), the results revealed net carbon emissions amounting to 13.71 tn CO2 eq ha−1, with the calculated emissions showing an increasing trend from the first year through the fifth year. Scope 1 (7.38 tn CO2 eq ha−1) and Scope 2 (3.71 tn CO2 eq ha−1) emissions emerged as the most significant, while irrigation (drip irrigation) and fertilizing practices were identified as the highest contributors to emissions. This study highlights the significance of using integrated digital tools for monitoring the performance of cultivations rather than standalone tools that are currently widely available. Integrated tools that incorporate various applications simplify data collection, encourage accurate record-keeping, and facilitate certification processes. By automating data entry and calculations, these tools reduce human error during agricultural carbon management and save time; thus, the integration of digital monitoring tools is vital in improving data accuracy, streamlining certification processes, and promoting eco-friendly practices, crucial for the evolving carbon market.