Differential sensing techniques are becoming nowadays an attractive alternative to classical selective recognition methods due to the “fingerprinting” possibility allowing identifying various analytes without the need to fabricate highly selective binding recognition sites. This work shows for the first time that surfactant-based ion-sensitive microspheres as optodes in the microscale can be designed as cross-sensitive materials; thus, they are perfect candidates as sensing elements for differential sensing. Four types of the newly developed chemosensory microspheres—anion- and cation-selective, sensitive toward amine- and hydroxyl moiety—exhibited a wide range of linear response (two to five orders of magnitude) in absorbance and/or fluorescence mode, great time stability (at least 2 months), as well as good fabrication repeatability. The array of four types of chemosensitive microspheres was capable of perfect pattern-based identification of eight neurotransmitters: dopamine, epinephrine, norepinephrine, γ-aminobutyric acid (GABA), acetylcholine, histamine, taurine, and phenylethylamine. Moreover, it allowed the quantification of neurotransmitters, also in mixtures. Its selectivity toward neurotransmitters was studied using α- and β-amino acids (Ala, Asp, Pro, Tyr, taurine) in simulated blood plasma solution. It was revealed that the chemosensory optode set could recognize subtle differences in the chemical structure based on the differential interaction of microspheres with various moieties present in the molecule. The presented method is simple, versatile, and convenient, and it could be adopted to various quantitative and qualitative analytical tasks due to the simple adjusting of microspheres components and measurement conditions.