In this paper, I explore the role of aggregate fluctuations as a persistent determinant of heterogeneity in firm-level markups. To analyze how business cycles generate dispersion in markups, I used a reduced-form model to estimate the effects of aggregate conditions close to listing on the age profiles of markups for a sample of U.S. listed companies. I then use the estimated markups to calibrate a general equilibrium model that features heterogeneous product markets, customer base accumulation and firm dynamics. A novel feature of the model is that firms can accumulate customers both by increasing sales as well as by making direct investments in customer acquisition, which is important to match the empirical findings. As the value of operating in each product market fluctuates endogenously with business cycles, aggregate conditions generate a selection on the product market composition of the cohorts of listing firms that results in time-varying heterogeneity in the cross-section of active companies. This heterogeneity is persistent and is able to significantly affect the response of the economy to future aggregate shocks and the co-movements of aggregate markups with output.