Carboxyl-enriched and size-selected polymer nanoparticles (NPs) may prove to be very useful in biomedical applications for linker-free binding of biomolecules and their transport to cells. In this study, we report about the synthesis of such NPs by low-pressure low-temperature pulsed plasma polymerization of acrylic acid. Gas aggregation cluster source was adapted to operate plasma with a constant pulse period of 50 μs and with varying duty cycle. The NPs were produced with the size ranging from 31 ± 5 to 93 ± 14 nm and with retention of the carboxyl groups ranging from 4.0 to 12.0 atom %. Two regimes of the NP formation were identified. In the large duty cycle regime, the NP growth was interfered with by positive ion bombardment which resulted in the ion-driven detachment of the carboxyl species and in the formation of carboxyl-deficient NPs. In the small duty cycle regime, the NP growth was accompanied by the radical-driven chain propagation with the attachment of intact monomer molecules. Improved efficacy of the monomer retention resulted in increased concentration of the carboxyl groups.