The objective of this data in brief article is to represent the associated data set regarding our published paper in Plant Science Nadeem et al., 2019. Data set represent soil acid phosphatase activity, association of individual molecular species of four major lipid classes with soybean forage quality indices when cultivated in boreal podzolic soils under cool climatic conditions. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidic acid (PA) and acylated glucosyl betasitosterol ester (AGIcSiE) molecular species grouped the soybean forage quality indices in different quadrants on principal component analyses. Furthermore, the total lipid profile and correlation of major lipid species with forage quality indices are included in this data in brief article. This data set support the main findings described in Nadeem et al., 2019.