This dataset includes field data collected from gardens plots in 38 urban gardens across the city of Boston in 9 neighborhoods: Dorchester, East Boston, Fenway, Hyde Park, Jamaica Plain, Mattapan, Mission Hill, Roxbury, and South End across 3 seasons: spring, summer, and fall (June 3-7, 2021; August 25-26, 2021; October 23-24, 2021). Neighborhood borders were defined by census tract block group designations available from the city (Department of Innovation and Technology 2021). Census data was taken from American Community Survey -1 year estimates for 2021 available from the U.S. Census Bureau. For each garden, all plots were hand mapped on site by researchers, enumerated, and then randomly selected using a number generator for further census. In each plot, every individual crop plant was counted and identified to species and cultivar if known or marked by gardeners. In addition, the number and species of each tree in the garden was surveyed. We identified each crop species (no ornamental, non-edible plants were surveyed other than communal garden trees) and classified each plant species as annual or perennial according to whether they could survive across multiple growing seasons in the temperate region and are practiced as perennial crops, ie. gardeners do not typically remove the entire plant at the end of growing season. Biennial and woody plants were all classified as perennial. We classified all crops according to USDA classifications as vegetable, fruit, grain, culinary, medicinal, and combinations of these classifications. We also include an R notebook with code used to generate figures and run analyses supporting the work entitled, "Rooting in place: Trees and perennials reflect permanence in urban gardens and communities" by the authors listed. A knitted html for R Markdown file is also included in PDF format.