<p>The importance of sustainable nutrient management has risen significantly to ensure agricultural productivity while preserving environmental health. This systematic review spanning 20 years (2005–2025) aggregates global research trends regarding Integrated Nutrient Management (INM) that utilizes natural and organic inputs and examines its effects on crop yield, soil quality, carbon capture, and energy efficiency. Using the PRISMA framework, bibliometric and scientometric analyses were performed in RStudio (Biblioshiny) and VOSviewer, based on 2,441 peer-reviewed articles indexed in SCOPUS. The findings indicate a marked increase in INM-related research over the past two decades, driven by both the overall growth in global scientific output and a rising focus on sustainable nutrient management. India and China emerged as the top contributors, highlighting the integrated application of organic resources like farmyard manure, compost, biofertilizers, and biochar. Research shows that INM practices improve soil organic carbon levels, microbial activity, and nutrient-use efficiency while achieving yields comparable to traditional farming methods. Additionally, energy evaluations and life-cycle assessments indicate lower greenhouse gas emissions and enhanced energy efficiency in organic-integrated systems. The evolution of research themes shows a movement towards nutrient management strategies that are climate-resilient and part of a circular bio-economy. Nonetheless, challenges such as regional disparities, methodological inconsistencies, and limited cross-scale analyses remain, hindering the translation of findings into global policies. This review highlights the necessity for standardized evaluation frameworks that incorporate biophysical, energetic, and ecological indicators to promote sustainable nutrient management.</p>