The objective of this paper is to evaluate the variations in the ability of Pistacia atlantica leaves to inhibit enzymes linked to type 2 diabetes (α-amylase and α-glucosidase) and to hypertension (angiotensin converting enzyme-I (ACE-I)), depending on harvesting month, gender and growing region, as well as to identify the peaks in chromatographic fingerprints that potentially correspond to components with enzymatic inhibitory activities. In this study, LC fingerprints of P. atlantica leave extracts were developed. Peaks which were probably responsible for the anti-amylase, anti-glucosidase and anti-ACE-I activities were assigned. For the latter purpose, the relevant information was extracted, linking the chromatographic fingerprints with the activities using a linear multivariate calibration technique, i.e., Partial Least Squares (PLS) regression. Prior to the construction of the models, the fingerprints are aligned using a warping method, called Correlation Optimized Warping (COW). Besides COW, different other data pretreatment methods were applied and compared. Our findings revealed that the influence of the growing region and gender on the α-amylase, α-glucosidase and ACE-I inhibitory activities of P. atlantica leaves was less important than the harvest time. Thirteen common peaks were selected from the chromatograms and used as a dataset to model the biological activities. The peaks potentially responsible for the biological activity of the samples were indicated by studying the regression coefficients of the models. Seven peaks corresponding to possibly anti-amylase compounds were found, while 6 peaks were considered important for inhibiting the α-glucosidase activity. Furthermore, the regression coefficients of the hypertension model indicated eight peaks as being important for inhibiting the ACE-I activity. The contributions of individual phenolic compounds of P. atlantica leaves to the α-amylase, α-glucosidase and ACE-I inhibitory activities were also identified. This investigation showed that the extract of P. atlantica leaves provides a rational basis for the isolation and development of antidiabetic and antihypertensive agents.