Mycobacterial HelD is a transcription factor that binds stalled RNA polymerase (RNAP), dissociates it from nucleic acids and, if present, the antibiotic rifampicin. The rescued RNAP, however, must disengage from HelD to participate in subsequent rounds of transcription. The mechanism of release is unknown. We show that HelD from Mycobacterium smegmatis forms a complex with RNAP associated with the primary sigma factor σA and transcription factor RbpA but not CarD. We solved a series of RNAP-σA-RbpA-HelD structures with or without promoter DNA. These snapshots capture HelD during transcription initiation, describing mechanistic aspects of HelD release from RNAP and its protective effect against rifampicin. Biochemical evidence supports these findings, defines the role of ATP binding and hydrolysis by HelD in the process, and confirms the rifampicin-protective effect of HelD. Taken together, HelD mediates an alternative pathway of transcription initiation where this process is protected from rifampicin until the last possible moment.