Background: Cloud forests are common in the Neotropics and an important part of its hydrological cycle. An investigation on how elevation and recovery from agriculture affects cloud forest floristics and physical structure in Ecuador was undertaken. Methods: Species and diameter at a specified height (dsh) of trees were sampled in large plots in Maquipucuna and Yanacocha cloud forests in Ecuador and also in smaller plots at Maquipucuna recovering after cropping in sugarcane (Saccharum officinarum L.) and banana (Musa sp.). Results: (1) Palicourea sp. was the only species found at both primary sites; Vernonia pallens Sch.Bip., Erythrina megistophylla Diels, Nectandra sp., and Miconia sp. were found in both primary and secondary plots at Maquipucuna; and Miconia sp. was the only species in common between the Maquipucuna secondary plots and the primary plot at Yanacocha Reserve. (2) The mean stem size was similar between the primary Maquipucuna plots and the Yanacocha plot, but the Yanacocha plot had more total stems and more stems in each size category, which lead to more basal area, above-ground biomass, and canopy closure at Yanacocha compared to Maquipucuna. (3) In the secondary plots, there were no stems larger than 29 cm dsh at breast height, which lead to a much smaller mean stem size and lower basal area, above-ground biomass, and canopy closure compared to the primary plots at both sites. Conclusions: For the primary cloud forest at Maquipucuna, an increase in elevation changed the species-level floristics more than conversion to and then abandonment from agriculture; however, while a rise in elevation increased the number of stems, agriculture reduced stem size structure.