Challenges of land scarcity, climate change and water shortage are contributing to escalating the shortage of protein rich food in sub-Saharan Africa. In Kenya a total of 27.8% of the population was undernourished, and a total of 72.3% were categorised as moderately or severe food insecure in 2021–2022. The need to investigate alternative protein sources with less impacts on land, water and climate change, which potentially could replace, at least some of the current production of livestock as the main protein source, is getting increasingly urgent. The main aim of this study is therefore to conduct an environmental footprint analysis of favourable protein production systems in Kenya to evaluate environmental impacts on land, water, and climate. The methodological approach used in this study is referred to as environmental footprint analysis, which is applied to assess; (1) farmed fish in ponds, (2) farmed fish in solar based affordable recirculation aquaculture systems (A-RAS), (3) dried spirulina (Arthrospira Platensis), and (4) chicken from semi-intensive farms. The results show that the most promising alternatives to cattle production are dried spirulina produced in ponds, followed by fish produced in affordable recirculation systems (A-RAS) run on solar energy. Spirulina fully replacing beef production would reduce water usage with 34.7 billion m3/year, land/water surface area with 34.8 thousand km2/year, and GHG emission with 28.2 megaton CO2eq/year. For fish farmed in A-RAS, such replacement would reduce water, land and emissions with 30.7 billion m3/year, 32.0 thousand km2/ year and 23.0 megaton CO2eq/year, respectively. This study illustrates that it is possible to tackle urgent challenges of food and nutrition security for millions of people in sub-Saharan Africa and worldwide with a sustainable protein transition towards a more sustainable, inclusive production system of small-scale farmers, if making use of alternative protein sources, such as from solar based A-RAS and microalgae.