Substance use disorder (SUD) affects the relationship and care of children, promoting abusive behaviors. The parental-filial relationship can improve with the development of parental competences (PC) in users of treatment programs for SUD. However, few programs prioritize intervention over these skills. The objective of this study is to verify the influence of SUD on the development of negligent behaviors and to analyze the influence of SUD treatment on PC, considering the previous trajectory of consumption and treatment (TCT), the legal situation (LS), and socio-family background (SFB). The sample is made up of 67 users of a SUD treatment program in Chile, with at least one child under the age of 12. One hundred percent of users engage in negligent behavior. After nine months of treatment, PCs improved significantly. TCT and SFBs influence the development and improvement of PCs.