Hosts and bacteria can enter into a number of different relationships, from mutualism, where both partners benefit, to exploitation, where one partner benefits at the expense of the other. Many host-microbe relationships have been presumed to be mutualistic but frequently only benefits to the host, and not the symbiont, have been considered. However, it is necessary to understand the fitness consequences on both partners to understand how symbioses persist over time and how different host-symbiont pairings can vary in their fitness outcomes. Here we test the effect of symbiosis on the fitness of two facultative symbionts (Burkholderia agricolaris and B. hayleyella) in the social amoeba Dictyostelium discoideum. Using two indicators of symbiont fitness, growth rate and abundance, we determined the effect of D. discoideum on Burkholderia fitness. We found that D. discoideum amoebas lowered the growth rate of both Burkholderia species in liquid culture. We tracked the abundance of Burkholderia grown with and without D. discoideum in soil microcosms over a month and found that B. hayleyella had larger populations when associating with D. discoideum while B. agricolaris was not significantly affected. Overall, we find that both B. agricolaris and B. hayleyella pay a cost to associate with D. discoideum, but B. hayleyella can also benefit under some conditions. Understanding how fitness varies in facultative symbionts will help us understand the persistence of host-symbiont relationships.