Phenolic-enriched extracts from Portuguese junipers were described as potential neuroprotective natural products. However, evaluation of plants for pharma/nutraceutical industry is based on secondary metabolite content, which is influenced by the environmental conditions. Therefore, it became important to elucidate the metabolic response of the junipers to seasonality and to stress conditions with regard to polyphenol production. Seasonal conditions modulated total phenolic and flavonoids contents of the four juniper species. Higher levels of phytochemicals were obtained when plants were not actively growing. However, only a few differences were registered in the relative contents of psydrin and a procyanidin dimer, according to species. Salt stress and methyl jasmonate elicitation promote different responses within the species. They were effective in enhancing phenolic accumulation, with just a few alterations in the relative contents of procyanidins, epicatechin, and quercetin derivatives. These differences were also reflected in gene expression of important enzymes from biosynthetic pathways.