Understanding the behavior of mycorrhiza-originated glomalin, either of plant or soil origin, is anticipated to facilitate better opportunities of modulating antioxidants and carbon distribution in plants. In this study, trifoliate orange seedlings with half of roots were colonized by Acaulospora scrobiculata and Funneliformis mosseae in a split-root rootbox. Mycorrhizal inoculation showed a significantly higher plant biomass of trifoliate orange, regardless of mycorrhizal species. Glomalin-related root protein showed a systematic increase in non-mycorrhiza-inoculated chamber under inoculation with A. scrobiculata and F. mosseae than under non-mycorrhizal inoculation. Similar increase was also observed in easily extractable glomalin-related soil protein and total glomalin-related soil protein as a result of F. mosseae colonization only. Mean weight diameter and soil organic carbon were significantly higher under mycorrhization than non-mycorrhization, irrespective of mycorrhized or non-mycorrhized chamber. Mycorrhizal inoculation stimulated an increase in soil protease activity in the mycorrhized chamber, without any distinctive change in the non-mycorrhized chamber. These results, hence, suggested that mycorrhization conferred a systematic increase in glomalin synthesis in roots and soils, collectively, aiding in better aggregate stability and soil carbon sequestration.