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Abstract Background Physical activity not only is beneficial to a person’s health, but can also have a positive influence on cognitive functioning. However, elderly people with chronic illness(es) often do not meet the physical activity guidelines. Physical activity programs for the elderly exist, but these are often expensive and not easily accessible to the elderly with chronic illness(es). In addition, the beneficial effects of these physical activity programs on cognitive functioning have never been specifically tested in this target group. Hence, this randomized controlled trial aims to test whether Active Plus, a proven effective physical activity intervention, is able to improve the cognitive functioning of elderly people with chronic illness(es) or to slow down cognitive decline. In addition, it studies what kind of activity, intensity, duration and frequency of physical activity most strongly influence cognitive functioning. Methods A randomized controlled trial is performed, comparing the Active Plus intervention group to a waiting list control group. In total 540 older adults (≥65 years) with at least one chronic illness that limits mobility are recruited from 7 municipalities. Comparable neighborhoods within a municipality are randomly allocated to the intervention or control group. Baseline and follow-up measurements after 6 and 12 months assess cognitive functioning and physical activity behavior, measured both objectively with an accelerometer and subjectively with a self-report questionnaire. Multilevel analyses are conducted to assess effects on cognitive functioning, including analyses on moderation effects for physical activity type, frequency, duration and intensity. Discussion To our knowledge this is the first study to investigate effectiveness of a physical activity program on cognitive functioning in elderly people suffering from a broad range of chronic illnesses. If proven effective Active Plus would be a very cost effective intervention not only to increase physical activity, but also to improve cognitive functioning or slow down cognitive decline. Up till now clear evidence is lacking on the kind of physical activity, intensity, duration and frequency needed to achieve cognitive benefits. By measuring both with accelerometers and self-report questionnaires we hope to gain insight in these processes. Trial registration Nederlands Trial Register NL6005; Date of Registration 21-03-2017.