This study contributes to the Climate, Land, Energy, and Water system (CLEWs) framework by developing an integrated model for Kenya capturing the interdependencies between climate, land, energy, and water systems. Focusing on cooking and crop production, it examines their contributions to land use changes, mainly deforestation, and emissions. We evaluate three scenarios-BAU, SC1, and SC2- that target clean cooking transitions and reduced crop imports, covering seven crops representing 72 % of Kenya's cultivated area. We detail the challenges of gathering data to populate such a model through document examination and literature review, and we identified uncertain input parameters. Results show that forest loss from cooking varies with the fraction of non-renewable biomass (fNRB). Under BAU, forest cover loss could range from 300 km2 at an fNRB of 0.3 to 900 km2 at 0.9. Scenarios SC1 and SC2 mitigate these impacts through cleaner cooking solutions. By 2050, under the clean cooking scenario (SC2), LPG stoves could achieve up to 96 % penetration, reducing CO2 emissions to 8.3 MTon and PM2.5 to 0.8 kTon, compared to high emissions in the BAU scenario dominated by wood and charcoal stoves. In agriculture, land use expands by 56 %, 69 %, and 33 % across the scenarios, while fossil fuel use rises from 2.46 PJ to 5.9 PJ by 2050, increasing CO2 emissions, from 183 kTon to 436 kTon. The findings highlight the need for integrated policies promoting clean cooking, sustainable agriculture, and deforestation mitigation. This integrated CLEWs approach provides actional insights for reducing deforestation and emissions in energy and agriculture sectors.