The aim of this work was to classify the business incubators in Spain according to the four phases of the startup’s incubation process. Considering that the graduation rate implies greater survival and business success of the incubated companies, they have been identified at each stage of the incubation (spread of entrepreneurship, pre-incubation, advanced incubation, and graduation). The activities that present higher impacts on the success of the incubated companies and the activities carried out by the business incubator that have a greater relevance on the graduation of the companies have concretely been considered. Principal component (PC) cluster analysis has been applied. All the incubation variables were used simultaneously, reducing their number and grouping them into factors. Finally, the cases were grouped according to these latent variables. Principal component analysis reduced dimensionality to eight factors with a 74% explained variance. Factor 1 was positively related to pre-incubation variables; factor 2 was linked to training and collaboration variables within the entrepreneurship diffusion phase. Factor 3, named activity monitoring and control, was related to phase 3, or basic incubation variables. Cluster analysis facilitates the grouping of business incubators into three clusters: Group 1 (16% of the total), incubators with strong deficits in incubation phases 1, 2, and 3. They are small-sized business incubators, often located in rural areas or cities, with a low graduation rate. Group 2 (30%), business incubators with a very high graduation rate and strongly positive values in factors 1 and 2. Factor 3, although positive, is susceptible to improvement. They are the largest group of business incubators and usually located in industrial and technological parks. Group 3 (54%) is the majority, with values close to clusters 2 and 3.