Predicting the bicycle flow capacity at signalized intersections of various characteristics is crucial for urban infrastructure design and traffic management. However, it is also a difficult task because of the large heterogeneity in cycling behavior and several limitations of traditional capacity estimation methods. This paper proposes several methodological improvements, illustrates them using high-resolution trajectory data collected at a busy signalized intersection in the Netherlands, and investigates the influence of key variables of capacity estimation. More specifically, it shows that the (virtual) sublane width has a significant effect on the shape of the headway distribution at the stop line. Furthermore, a new method is proposed to calculate the saturation headway (a key variable determining capacity), which excludes the cyclists initially located close to the stop line using a distance-based rule instead of a fixed number (as is usually done in practice). It is also shown that the saturation headway is quite sensitive to the sublane width. Moreover, a new, empirically based method is proposed to identify the number of sublanes that can be accommodated in a given cycle path, which is another key influencing variable. This method yields considerably lower estimates of the number of sublanes than traditional methods, which rely solely on the (available) cycle path width. Finally, the authors show that methodological choices such as the sublane width and the method used to estimate the number of sublanes have a considerable effect on capacity estimates. Therefore, this paper highlights the need to define a sound methodology to estimate bicycle flow capacity at signalized intersections and proposes some steps to move toward that direction.