The biggest disadvantage of fluorescence spectroscopy is that all molecules are not fluorescent so its use is limited to fluorescent molecules. 

Another disadvantage is that it is susceptible to the auto-fluorescence of the sample as well as to changes in the oxygen and pH levels of the sample.  

The shorter lifespan of fluorophores and loss of recognition capability and photo-stability are other disadvantages of fluorescence spectrometry. 

Foreign material in the biological media can also cause issues related to potential toxicity.