A new format of solid phase microextraction (SPME), boronate affinity SPME, was proposed for the first time for covalent extraction of cis-diol containing biomolecules. This new SPME format is based on the reversible complex formation between boronic acids and 1,2- and 1,3-cis-diols. The complex formation and dissociation can be facilely controlled by changing pH. An extracting phase of poly-3-aminophenylboronate (polyAPBA) electrochemically deposited on a metal wire was employed to demonstrate the concept of this new methodology. Catechol and riboflavin were used as the test analytes, and the SPME extraction was combined off-line with high-performance liquid chromatographic (HPLC) separation followed by UV absorbance or fluorescence detection. Fundamental aspects, such as selectivity, extraction/desorption equilibrium, linearity, effect of competing compounds, reproducibility and life-time, were first investigated. Then the developed method was applied to beer samples since the content of riboflavin plays an important role in the flavor stability of beverages. Excellent performance of the SPME fibers was observed for both standard and real samples. Particularly, the expected excellent features of the polyAPBA extracting phase were experimentally verified, which include specific selectivity, eliminated matrix effect and manipulable capture/release. The new methodology of SPME can be a promising tool since a lot of 1,2- and 1,3-cis-diol-containing compounds are of great biological importance.