The whitefly Bemisia tabaci Middle East-Asia Minor 1 (MEAM1), previously known as B biotype, is a major agricultural pest with a reputation for developing resistance to insecticides. DNA-based identification revealed that B. tabaci MEAM1 is the dominant species within Australian cotton cropping. Discriminating doses of 10 mg/L for pyriproxyfen and 300 mg/L for both diafenthiuron and bifenthrin were determined from bioassay data collected in 2010–2015. Resistance to these insecticides was tested in whitefly populations collected in 2017 from cotton crops in Queensland and New South Wales. This study reports on the presence of pyriproxyfen resistance in B. tabaci MEAM1 at seven locations in Queensland and New South Wales. One population from Goondiwindi was resistant to bifenthrin, whereas no populations tested had resistance to diafenthiuron. To determine the presence of resistance alleles to organophosphates and pyrethroids, reference populations of susceptible and resistant whiteflies (pyriproxyfen, bifenthrin and neonicotinoid) were tested. The resistance mutation L925I was found in a pyrethroid-resistant population and in some individuals from the pyriproxyfen-resistant population. The mutation F331W that confers organophosphate and carbamate resistance was found in all individuals tested including the susceptible reference population, indicative of a widespread distribution in Australian B. tabaci MEAM1. The cotton industry has revised the insecticide resistance management strategy for B. tabaci, to restrict the usage of pyriproxyfen to a single application within a 30-day window. Our results argue against the use of organophosphate and carbamate insecticides in Australian cotton, because B. tabaci MEAM1 populations show significant resistance levels. Furthermore, both pesticide groups are highly disruptive to a diverse range of natural enemy populations, and as such, widespread use likely contributes to pest outbreaks.