The suitability of Madrid as the capital of Spain is analyzed from different perspectives, questioning the belief that this choice was eminently personal or political but lacked economic rationality. The paper analyzes Madrid’s advantages over other possible capitals from the point of view of both intrinsic characteristics and those that depend on the transport network, such as the problem of supplies or the impact on the development of the surrounding territory. To deal with these questions it is necessary to consider logistical aspects that require an adjusted view of the existing transport network at that time. Using little-known primary sources and a novel methodology based on Delaunay triangulation, the 16th century Spanish transport network is reconstructed with a much higher level of accuracy than ever before. With this information, two maps are prepared that could be used for logistical analysis from a complex network perspective. The first map evaluates the real effects of the choice using an adjusted representation of the territory whilst the second map aims at avoiding the common fallacy of judging decisions made in the past applying current geographical know-how. This map, constructed with the planimetry of the 16th century, indicates how the somewhat deficient knowledge of Philip II with respect to the geographical reality of the day may have favored the choice of Madrid over Toledo, converting some Mediterranean coastal cities into more attractive options. The choice of Madrid as capital appears to be very reasonable in view of the different criteria used. Regarding supply difficulties, our results depart from traditional inclinations by deliberating the fact that the absence of a port in Madrid does not pose an insuperable problem. The latter is the case given that the advantages of maritime transport are far fewer than those usually considered, with Madrid’s geographical position offering significant advantages in terms of road transport.