Background The objective of this study is to evaluate titanium decontamination after different protocols while assessing changes in surface roughness, chemical composition, and wettability. Methods Ninety‐six smooth (S) and 96 minimally rough (R) titanium microimplants were used. Pristine microimplants were reserved for negative control (S‐nC/R‐nC, n = 9), while the remaining microimplants were incubated in Escherichia coli culture. Non‐decontaminated microimplants were used as positive control (S‐pC/R‐pC, n = 3). The other microimplants were divided into seven different decontamination protocols (12 S/R per group): 24% EDTA, 2% chlorhexidine (CHL), gauze soaked in 2% chlorhexidine (GCHL), gauze soaked in ultrapure water (GMQ), scaling (SC), titanium brush (TiB), and implantoplasty (IP). Contaminated areas were assessed by scanning electron microscope images, chemical composition by energy dispersive X‐ray spectroscopy, wettability by meniscus technique, and roughness by an optical profiler. Results Higher residual bacteria were observed in R‐pC compared with S‐pC (P <0.0001). When comparing S and R with their respective pC groups, the best results were obtained with GCHL, SC, TiB, and IP, with no difference between these protocols (P >0.05). Changes in surface roughness were observed after all treatments, with S/R‐IP presenting the smoother and a less hydrophilic surface (P <0.05). Apart from IP protocol, all the other groups presented a more hydrophilic surface in R than in S microimplants (P <0.003). All decontamination protocols resulted in a lower percentage of superficial Ti when compared with S/R‐nC (P <0.002). Conclusions All decontamination protocols resulted in changes in roughness, wettability, and chemical composition, but GCHL, SC, TiB, an IP presented the best decontamination outcomes.