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Spectinomycin selectively inhibits protein synthesis in cells and in extracts of Escherichia coli . When added to an exponentially growing culture, spectinomycin (50 μg/mL) rapidly and reversibly inhibits growth of Escherichia coli . Amino acid incorporation is slowed immediately but RNA synthesis continued. In extracts of Escherichia coli B, spectinomycin inhibits polypeptide synthesis directed either by endogenous messenger RNA or by MS-2 bacteriophage RNA. Maximum inhibition (70 to 80%) is achieved at 1 μg/mL (3 μM). . Spectinomycin blocks the translocation of peptidyl-tRNAs from the A-site to the P-site by inhibiting the binding of elongation factor G to the ribosome. Spectinomycin interacts specifically with the residues G1064 and 01192 in 16S rRNA and potentially change this molecule into an inactive conformation. Spectinomycin acts as a mixed noncompetitive inhibitor for the td intron RNA with a K _i of 7.2 mM. The splicing inhibition by spectinomycin is dependent on pH changes and Mg ²⁺ concentration, indicating electrostatic interactions with the intron RNA.

Renal excretion is a major elimination pathway for spectinomycin. Following IV administration, approximately 55% of the drug is excreted into the urine in unchanged form. After IV administration of 10 mg/kg spectinomycin shows a peak plasma concentration of 37.8 μg/mL and a systemic exposure (area-under the curve AUC _0-∞ ) of 15.7 μg/mL. Following single dose intramuscular administration, the overall elimination half-life of spectinomycin is 1.2 h in cattle, 1.0 h in sheep, 1.0 h in pigs, 1.65 h in chicken and 1.85 h in humans.