In vitro evaluations are essential to gaining a better understanding of re-osseointegration, while reducing animal use and the overall costs of peri-implantitis studies. This pilot study evaluated preosteoblast migration from 3-D-printed scaffolds to decontaminated titanium microimplants, creating a system that tries to mimic the bone–implant interface. Smooth (S) and minimally rough (R) titanium microimplants were incubated in Escherichia coli cultures and divided into six groups according to the decontamination protocol applied: EDTA gel (EDTA); chlorhexidine (CHL); chlorhexidine-soaked gauze (GCHL); scaling (SC); titanium brush (TiB); and implantoplasty (IP). Pristine S and R microimplants were used as the controls (C). After the decontamination procedures, the microimplants were inserted in 3-D-printed polyurethane-based scaffolds previously inoculated with preosteoblast cell cultures. Cellular migration was assessed after 24, 72 and 120 hours by ATP quantification. At the 120-hour time point, there was no statistically significant difference between S-C, S-EDTA, S-CHL, S-GCHL and S-SC ( p > 0.05), and between R-C, R-EDTA and R-GCHL ( p > 0.05). The in vitro model developed in this pilot study successfully demonstrated cell migration on the different decontaminated surfaces. This methodology suggests that on smooth microimplants, EDTA, GCHL, SC and TiB decontamination may have a reduced impact on preosteoblast migration, while on minimally rough microimplants, EDTA and GCHL decontamination affected cell migration the least. However, when selecting a decontamination protocol, the effectiveness of the decontamination per se must also be considered.