Objectives. To evaluate the internal adaptation of recent pulp capping materials (TheraCal and Biodentine) relative to MTA when used as indirect pulp capping for primary teeth. Materials and Methods. Thirty primary molars were randomly allocated into three groups, group (A) was TheraCal, group (B) was Biodentine, and MTA was the control group (C). A standardized round class-V cavity (1.5 mm diameter and 2 mm depth) was prepared using a milling machine on the buccal surface of each tooth with the pulpal floor located on the dentin. Then, pulp-capping materials were applied. Finally, all teeth were restored by composite restoration. The internal adaptation of the pulp-capping materials to the dentinal surface was investigated by microcomputed tomography (Micro-CT) to determine the internal gap volume, and by optical coherence tomography (OCT) to determine the high-intensity reflection of light from the floor. Results. Based on Micro-CT findings, TheraCal showed significantly higher internal gap volume than both MTA and Biodentine (
p
<
0.001
), while MTA and Biodentine did not show a significant difference in the gap volume. Based on the OCT findings, TheraCal showed a significantly higher intensity of light reflection than both MTA and Biodentine (
p
<
0.001
); however, there was no significant difference between MTA and Biodentine. Pearson’s correlation test showed that there was a strong positive correlation between Micro-CT and OCT (
r
=
0.686
,
N
=
30
,
p
<
0.001
). Conclusions. Biodentine and MTA showed a comparable result in terms of their internal adaptation on the dentinal surface of the primary teeth, and both were better than TheraCal. There is a moderate to a strong positive correlation between Micro-CT and OCT in the measurement of internal adaptation of the tested pulp capping materials. OCT can be helpful and beneficial for the clinical setting and allow dentists to screen and evaluate restorations during follow-up.