In view of climate change and the active extension of soybean cultivation in Russia, the identification of yield-limiting factors has become a relevant task. The objective of this study was to identify the climatic factors associated with the variation in soybean productivity under the contrasting eco-geographical conditions of the Krasnodar (KR) and Primorye (PR) territories of Russia. An analysis of 424 soybean varieties from the global collection of the N.I. Vavilov Institute (VIR) at experimental stations in KR and PR in 1987–2005 showed that the soybean yields were higher and time to maturity was longer in KR than in PR, while the 1000 seed weight, on average, was irrelevant to the place of cultivation. The agrometeorological regression models of the observations in 1972–2017 of varieties accepted as the standards showed that the yield in PR was positively related to the sum of the temperatures above 10 °C and negatively related to precipitation in October, while in KR it was positively related to the hydrothermal coefficient. The stability of the soybean yield and of the time to maturity were higher in PR than in KR. Under the conditions of increasing temperatures and the absence of reliable trends for precipitation, a lack of moisture becomes a significant disadvantage for soybean in KR, while in PR conditions are improving.