Colombia is one of the world’s leading flower-producing and exporting countries. As a result, many people, including small farmers, work in flower production, contributing significantly to local communities’ economic stability. This study focused on analyzing the development of musculoskeletal pain in 37 Colombian flower growers at the beginning and end of a typical workday. This cross-sectional study used a body map to record pain in 21 body parts and a visual analog scale to measure pain intensity. The Wilcoxon signed-rank test analyzed changes in musculoskeletal pain intensity between the beginning and end of the workday, categorizing pain as mild (≤10 mm), moderate (>10 mm and ≤20 mm), or severe (>20 mm). Additionally, changes were further classified based on the percentage increase in pain, with mild (≤25%), moderate (>25% and ≤50%), and severe (>50%) levels. Significant increases in musculoskeletal pain were observed in 17 body parts, with the highest increases reported in the right hand-wrist, right ankle-foot, lower back, and right shoulder. The intensity of musculoskeletal pain at the end of the workday was moderate for 15 body parts, while for six body parts, it was mild. The average percentage change of musculoskeletal pain was severe in 20 body parts, while in the left elbow, it was moderate. The study underscores the importance of implementing ergonomic improvements in work practices to prevent musculoskeletal disorders, thereby enhancing the health and productivity of workers in this key export industry.