Botrytis cinerea (gray mold) and Penicillium expansum (blue mold), are major pome fruit postharvest pathogens and their control relies heavily on the use of one postharvest fungicide (fludioxonil). This study aimed to evaluate the efficacy of the cyclolipopeptides (CLPs), in the form of fengycin and iturin A, in crude metabolite extracts from Bacillus amyloliquefaciens as an alternative biofungicide. The crude extract containing CLPs was applied with an edible coating (i.e., zein as a carrier) as a postharvest treatment against B. cinerea on “Packham’s Triumph” pears and P. expansum on “Cripps Pink” apples. Treatments were applied either as dips in combination with a zein edible coating at pH 2.0 or pH 8.0, or as sprays with a zein edible coating at pH 2.0 or pH 8.0. The efficacy of CLP applications was measured in comparison to the standard registered synthetic fungicide fludioxonil at a concentration of 299.0 mg/L. Treatments were applied to the fruit either preventatively (as sprays) or curatively (as dips or sprays). The lowest mean blue mold incidence (68.6%) was achieved when the edible coating containing the crude extract of B. amyloliquefaciens (CLP at pH 2.0) was applied as a curative dip treatment. B. cinerea infection was reduced by 92.6%, resulting in a 5.7% gray mold incidence for the curative application of CLPs at pH 2.0. This result was not significantly different from the inhibitory action of the fungicide fludioxonil. These results indicate that CLPs are an effective alternative biofungicide that can be used for the control of B. cinerea on pome fruit, especially if their formulation and application are improved and optimized.