Basin modeling in structurally complex areas involves several difficulties associated with its geometric and thermal history approaches. There have been multiple developments concerning the structural geometry in doing three-dimensional (3-D) basin modeling in these settings. However, their applicability is limited because most of these improvements require 3-D structural restorations, which is an input that is not always available at basin scale. Although a traditional basin model using backstripping could give a faster overview of the petroleum system elements, it is an alternative method that may distort the structural evolution and, consequently, the petroleum potential evaluation. Equally important are the thermal history uncertainties in these environments, where several factors disturb the thermal regime. Despite these difficulties, traditional 3-D basin modeling could be a reliable tool when we are able to understand the geometric and thermal histories and implement the proper adjustments. We propose alternative methods to tackle common problems when building 3-D basin models, and we demonstrate their validity with an example in the Middle Magdalena Valley, Colombia. This hydrocarbon province located in the northern Andes corresponds to an intermountain basin that has undergone a complex evolution. Its structural configuration represents a modeling challenge by means of the backstripping method. Additionally, a high variability exists in the present-day basal heat flow related to its structural evolution. The result of our model not only fits the calibration data, but also reflects the geological processes better. The proposed methodology intends to aid basin modelers in providing additional options when modeling in structurally deformed basins.