You need to wait for the promise to return a value before making the http request. You could put your token logic into its own function that returns a promise, and then start an observable using the RxJS from function. Once the promise returns a value you can then use switchMap to make your http request.

I have included your map in the RxJS pipe, although it's doing nothing at the moment.

export class GroupsService {

  token: any;

  constructor(
    private storageIonic: NativeStorage,
    private env: EnvService,
    private http: HttpClient,
  ) {
  }

  getGroups(): Observable<any> {
    return from(this.getToken()).pipe(
      switchMap(() => {
        const httpOptions = {
          headers: new HttpHeaders({
            Authorization : this.token,  //sending token to server
            Accept: 'application/json, text/plain',
            'Content-Type': 'application/json'
          })
        };

        return this.http.get(`${this.env.GROUPS}`, httpOptions);
      }),
      map(groups => groups)
    );          
  }

  private getToken(): Promise<any> {
    if (this.token) {
      return new Promise((resolve, reject) => resolve(this.token));    
    }

    return this.storageIonic.getItem('token')
      .then((token) => {
          this.token = token.access_token;
      }).catch(error => console.error(error));
  }
}

 this.storageIonic.getItem('token').then((token) => {
            this.token = token.access_token;
        }).catch(error => console.error(error));
 }

This call is asychronous, you will not get the token in the next line Try it out like this

export class GroupsService {

    token: any;

    constructor(
        private storageIonic: NativeStorage,
        private env: EnvService,
        private http: HttpClient,
    ) {
        // Get token
        this.storageIonic.getItem('token').then((token) => {
            this.token = token.access_token;
        }).catch(error => console.error(error));
    }

    getGroups(): Observable < any > {
        // I also add this here to make sure that i will get token in any case, yet it's returning undefined
        let response = new Observable<any>();
        if (this.token === undefined) {
            this.storageIonic.getItem('token').then((token) => {
                this.token = token.access_token;

                console.log('token: ', this.token); // undefined
                const httpOptions = {
                    headers: new HttpHeaders({
                        Authorization: this.token, //sending token to server
                        Accept: 'application/json, text/plain',
                        'Content-Type': 'application/json'
                    })
                };
                response = this.http.get(`${this.env.GROUPS}`, httpOptions).pipe(
                    map(groups => groups)
                );
            }).catch(error => console.error(error));
        }

        return response;

    }
}

I am not sure about the source of your problem but you may want to change your observables to promises as I have explained in the comments.

    getGroups(): Promise<any> {
        // I also add this here to make sure that i will get token in any case, yet it's returning undefined
        if (this.token === undefined) {
        this.storageIonic.getItem('token').then((token) => {
            this.token = token.access_token;
        }).catch(error => console.error(error));
        }

        console.log('token: ', this.token);  // undefined
        const httpOptions = {
        headers: new HttpHeaders({
            Authorization : this.token,  //sending token to server
            Accept: 'application/json, text/plain',
            'Content-Type': 'application/json'
        })
        };
        return this.http.get(`${this.env.GROUPS}`, httpOptions).toPromise();
        // Also probably the below one works too, you can try to find the proper syntax, it was something like this
        return this.http.get(`${this.env.GROUPS}`, httpOptions).pipe(
        map(groups => groups)
        ).toPromise();
    }

I have changed some lines. (Change method signature, Observable => Promise and add toPromise() to return line)

You can call the method like below.

const response = await getGroups(); // This one will return the response of the request. 
If you debug the code you will see that your code will wait here until it gets a response.

// IF YOU DO LIKE BELOW IT WON'T MAKE ANY SENSE
const response = getGroups(); // This will not make the call, it will just return the request object.
// In order to do the operation defined in a promise, you must call it with await prefix.

You may need apply the solution above to other parts of your code too. E.g. you are initializing the token under the constructor which it is not a good practice as I know, you may want to move that initialization under onInit() and make onInit function async. This way you can make sure that token is defined when you are making the call, otherwise your token may not beer initialized while you are making the request. And since you are not waiting your code in undefined check same thing will happen again. (Convert your storageIonic.getItem(token: string) function to a promise and return the token from that function)