Methods for detecting the presence of an analyte in a sample are provided. Aspects of the methods include mixing a sample with an indirectly-detectable labeled binding member that includes a label moiety. The mixing produces a first composition. Unbound labeled binding member is then separated from any resultant binding complexes to produce a second composition that includes the binding complexes. A second light emitted by a light wavelength converter that is excited by a first light generated by the labeled binding member of the binding complexes of the second composition is then detected to detect the presence of the analyte in the sample. Embodiments also include kits and systems that find use in practicing the subject methods.