Starvation induces Myxococcus xanthus multicellular development. Rod-shaped cells move, forming mounds. Within mounds, rods differentiate into round, stress-resistant spores. Csignaling is proposed to activate FruA, which binds DNA cooperatively with MrpC to increase transcription of many genes. We report that the regulation of late-acting operons involved in spore metabolism (fadIJ) and coat biogenesis (exoA-I, exoL-P, nfsA-H) is more complex. These operons appear to be negatively regulated by FruA prior to its activation, then positively regulated by Csignal-activated FruA, based on transcript levels in mutants. Although MrpC is required to produce FruA, loss of MrpC affected transcript levels differentially. Transcript measurements also indicated that transcription factor Nla6 is a positive regulator of late-acting operons, whereas the DevI component of a CRISPR-Cas system is a negative regulator. FruA bound to all four promoter regions in vitro, but each promoter was unique in terms of whether or not MrpC and/or Nla6 bound, and in terms of cooperative binding. Whereas FruA switches from negative to positive regulation of all four operons temporally, MrpC and Nla6 appear to exert operon-specific temporal regulation. We propose that complex, differential regulation of late-acting operons ensures that spore resistance and surface characteristics meet environmental demands.