Between 1979 and 1985 Loubser conducted ethno-archaeological work on a a variety of  stone-walled settlements that were built by Bantu-speaking agriculturalists in South Africa, including Sotho-Tswana sites in Gauteng, Ndebele sites in Polokwane, and Venda sites in the Soutpansberg.  His other excavations in South Africa include an Early Iron Age site on the Tugela River, a Late Stone Age site on the Riet River, and a historic period site at Breyten. All these projects resulted in a better understanding of culture history sequences, settlement layouts, and oral histories.

Since he emigrated from South Africa to Georgia in 1993, Loubser has been conducting CRM archaeology and rock art work in the United States of America.  His archaeological work in the southeastern United States, primarily as a Principal Investigator with New South Associates, Inc., included a variety of Phase I surveys, Phase II test excavations, and Phase III data recoveries in Georgia, Florida, North and South Carolina, and Alabama, specializing in the Woodland  and Mississippian periods.  As an independent archaeologist with Stratum  Unlimited LLC since 2006, Loubser has been leading excavations in Oregon, western North Carolina, and northeastern Georgia. He also partook as consultant in archaeological fieldwork projects in California, Hawaii, Idaho, and North Carolina. He has authored and co-authored 200 reports concerning CRM work in the United States.

During his position as head of the Rock Art Department at the National Museum in South Africa, between 1987 and 1993, Loubser  recorded over 200 painted rock shelters in the Caledon River valley.  While in Australia in 1989, he gained considerable experience concerning rock art site conservation and management.  Loubser has worked  on  graffiti removal and rock art condition assessment projects with the Getty Conservation Institute (GCI) in 1989 (Australia), 1991 (California), 1994 (Baja California), 1995 (Baja California), and 1996 (Baja California). Through the years Loubser has shared his experience in rock art conservation and management with  archaeologists, rock art specialists, government agency personnel, and the general public, both in the field and at conferences and workshops in South Africa, Bolivia, France, Jamaica, Mexico, and across the United States of America. Loubser has thoroughly mapped, recorded, and sequenced 20 rock art sites on the Carrizo Plain for the Bureau of Land Management. In collaboration with archaeologists from the Forest Service and various volunteers, Loubser has also mapped, recorded, and sequenced 28 petroglyph sites in Georgia and the Carolinas.

In order to disseminate the results of his CRM-related work, Loubser publishes summaries of his research in books and journals. Among the publishers of Loubser's books and book chapters are AltaMira Press, Left Coast Press, Cambridge University Press, The University of Alabama Press, The University of Arizona Press, Wits University Press, and the South African National Museum.  Journals that have published articles by Loubser include Advances in World Archaeology, Cambridge Archaeological Journal, South African Journal of Science, The South African Archaeological Bulletin, Southern African Humanities, Time & Mind, American Anthropologist, American Indian Culture and Research Journal, and Early Georgia.  Loubser has authored and co-authored 110 articles and chapters.

Johannes Loubser is former co-chair of Society for American Archaeology Rock Art Interest Group, former Committee Member of Society for American Archaeology Excellence in Analysis Award, and former Vice-President of Georgia Council of Professional Archaeologists.  Special awards bestowed on Loubser include the Honorary Title of Distinguished Visitor from the town of Sucre in Bolivia and Merit Award for Archaeology from the University of the Witwatersrand in South Africa.  Loubser is on the editorial team of Time & Mind.