Background and Objectives: The increase in indications for hematopoietic cell transplants (HCTs) has led to the development of new care options after said transplant, such as home care after transplantation, which improves the patients’ quality of life. The main purpose of this research is to analyze the differences in the appearance of post-transplant complications between patients having underwent autologous HCT with at-home post-transplant modalities and those under in-hospital post-transplant care. Materials and Methods: An observational, analytical, longitudinal, and retrospective study of cases and controls. All transplanted people in the domiciliary model since 2020 are included as cases (20 subjects). For each case, two controls (40 subjects) are proposed among patients who received an autologous transplant in a hospital in the last five years with a similar demographic and pathological base profile in each case. Results: No significant differences were found between cases and controls, except for the Karnofsky value, which was higher in people receiving home treatment (91.7% vs. 87.74%; p = 0.05). The average number of days of the process post-transplantation was more significant at home (processing days 22.4 ± 2.6; post-transplantation days of 16.4 ± 2.08 versus 21.21 ± 4.18, with a mean of 15.51 ± 3.96 days post-transplant (days of the process p = 0.022; days post-transplant p = 0.002)). There is a more significant presence of neutropenic fever, mucositis, and positive blood cultures in the post-transplant patients who remain in the hospital. In contrast, the patients receiving home care post-transplantation undergo significantly more weight loss. Regarding the odds ratio of the appearance of adverse events, in the hospital setting, it is up to 8.5 times more likely to encounter neutropenic fever, 4.63 times more likely for mucositis, and 6.65 times more likely for the presence of pathogens in blood cultures. Conclusions: The home care modality in the post-transplant phase does not show an inferiority in conditions in the management and safety of the patient concerning the appearance of adverse events. However, more significant weight loss is detected in patients at home, and an increased risk of episodes of neutropenic fever, mucositis, and positive blood cultures for patients in hospital settings.