In this study, we evaluated how different procedures of calcium phosphate synthesis and its incorporation in collagen:chitosan scaffolds could affect their structural and thermal properties, aiming the obtention of homogeneous scaffolds which can act as drug delivery vehicles in bone tissue engineering. Therefore, three different scaffold preparation procedures were developed, changing the order of addition of the components: in CC-CNPM1 and CC-CNPM2, calcium phosphate synthesis was performed in situ in the chitosan gel (1%, w/w) followed by mixture with collagen (1%, w/w), with changes in the reagents used for calcium phosphate formation; in CC-CNPM3 procedure, calcium phosphate was synthesized ex situ and then incorporated into the collagen gel, in which chitosan in powder was mixed. In all procedures, 5% (in dry mass) of ciprofloxacin was incorporated. FTIR analysis confirmed the presence of calcium phosphate in all scaffolds. DSC curves showed that collagen denaturation temperature (Td) increased with calcium incorporation. SEM photomicrographs of scaffolds cross-section revealed porous scaffolds with calcium phosphate grains internally distributed in the polymeric matrix. XRD diffractograms indicated that the calcium phosphates obtained are hydroxyapatite. The pore size distribution was more homogeneous for CC-CNPM3, which also stood out for its smaller porosity and lower absorption in PBS. These results indicate that the in situ or ex situ phosphate incorporation in the scaffolds had a great influence on its structural properties, which also had consequences for ciprofloxacin release. CC-CNPM3 released a smaller amount of antibiotic (30%), but its release profile was better described by all the tested models.