Background: Gardening activities became increasingly popular in health promotion. The aim of this systematic review was to investigate the effect of gardening-based training or horticultural therapy on domains of health, including mental, physical and general health. Method: The MEDLINE, PsychINFO, Web of Science, Cochrane, EMBASE, Greenfile, CINAHL, WHO ICTRP, and Clinicaltrials.gov databases were searched from their inception to September 2023. Peer-reviewed, randomized controlled trials (RCTs) or experimental studies with intervention and control groups in English that evaluated the effect of gardening activity or horticultural therapy on health domains. Adult participants living with chronic conditions were selected. Author, year, location, sample size, participant characteristics, study characteristics, type of intervention, measurement time points, measured outcomes, measurements, effect sizes and p values were extracted. Results: Twenty-three studies (n = 4535) with 13 RCTs and 10 quasi-experimental studies were included. The participants had a mean age of 54.39 years, and the majority of them were females (63.25%). Types of chronic conditions included physical dysfunction, pain, obesity, anxiety, depression, hypertension, cognition disfunction, etc. The effects of gardening activities were compared with those of the control by categorizing health into three domains: mental health (SMD = -0.31; 95% CI: -0.97, 0.34), physical health (SMD = -0.25; 95% CI: -0.62, 0.11) and general health (SMD = -0.08; 95% CI: -0.20, 0.05). Conclusions: Gardening-based training programs have a small-to-medium effect on mental health in people living with chronic conditions. Relatively small effects were found for physical health and general health. Future research is recommended to better understand the impact of gardening activities on health. Trial registration: This systematic review is registered to PROSPERO (https://www.crd.york.ac.uk/prospero/) with registration ID: CRD42024504948.