Lecoq de Boisbaudran's early investigations focused on understanding the phenomenon of supersaturation, in which substances can exist in solution in higher concentrations than is possible under normal conditions. He showed that contact of supersaturated solutions with crystals of an isomorphous salt causes the substance to precipitate from the solution. He further showed that many anhydrous salts can be dissolved to create a supersaturated solution. These investigations were carried out from 1866 to 1869.
In 1874 Lecoq de Boisbaudran found that certain crystal faces dissolve more rapidly than other crystal faces. Specifically, he found that octahedral faces are less readily soluble than cubic faces in the case of ammonium alum crystals.
Lecoq de Boisbaudran made major contributions to the then-new science of spectroscopy, which relates to the interaction of light and matter. He applied spectroscopy to characterize elements, particularly the rare-earth elements. He developed a theoretical framework of spectroscopy, based on molecular vibrations. Theorizing that spectral frequencies relate to the atomic weight of an element, he recognized spectral trends based upon atomic masses.
Boisbaudran developed new experimental apparatus and used these to carry out spectral analyses of various chemical elements. Through systematic experimentation, he analysed spectra of 35 elements, using the Bunsen burner, electric spark or both to induce luminescence of samples of the elements. The results of his early investigations were published in his Spectres lumineux : spectres prismatiques et en longueurs dondes destinés aux recherches de chimie minérale' (1874).
To observe spark spectra in his experimental protocols, he typically placed a solution of a salt in a sealed glass tube, with a platinum wire in the solution as a negative pole, and another platinum wire above the surface of the liquid as a positive pole. In 1885, he experimented with reversing the polarity of the electric current.  In this way, he obtained phosphorescent bands in the spectra providing further insight into the spectral characteristics of various chemical elements. Using this apparatus, he discovered the lanthanides samarium (1880), dysprosium (1886) and europium (1890). In 1885, he also spectroscopically characterized gadolinium in 1885, an element previously discovered in 1880 by J. C. Galissard de Marignac.