Bioenergy has emerged as a promising alternative to fossil fuels due to its potential for renewable, carbon-neutral energy production. However, the geo-environmental implications of large-scale biomass cultivation require thorough evaluation. This chapter employs a systematic review methodology aligned with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to compare the environmental performance of bioenergy versus conventional fossil fuels, focusing on indicators such as soil quality, biodiversity, water resources, carbon sequestration, and phytoremediation potential. An initial pool of 7764 records was screened across major academic databases, yielding 46 peer-reviewed studies for qualitative synthesis. Results indicate that bioenergy systems sourced from residues and perennial feedstocks can reduce lifecycle greenhouse gas emissions and improve soil organic matter, yet they may also intensify water use and nutrient runoff if managed unsustainably. Land-use changes for dedicated energy crops can threaten biodiversity and alter hydrological cycles, though integrated practices—such as co-cultivation on marginal lands and adoption of conservation agriculture—mitigate these risks. Comparative analysis reveals that fossil fuel extraction and combustion produce higher direct CO₂, CH₄, and toxic pollutant emissions, alongside severe land degradation from mining and drilling activities. The chapter concludes that bioenergy’s environmental benefits are contingent on feedstock choice, site management, and policy frameworks that internalise indirect land-use changes and ecosystem service trade-offs. Strategic deployment of second-generation biofuels, combined with robust sustainability criteria, is essential to realise bioenergy’s role in a low-carbon energy transition without compromising food security or ecological integrity.